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Migrating bioinformatics questions from the Bioinformatics SE chat
There's a little bit of frustration in chat with regards to people asking questions that would be better asked in the main site. See here, for example. Some people can be encouraged to re-ask the questions themselves, but some prefer leaving the questions along in the chat interface.
How much emphasis should we put into migrating questions?

This is an issue across the SE network. Many people will ask in chat instead of the site. This is annoying for various reasons:

When asking in chat, nobody else benefits from the answer. The site doesn't gain any new content and someone with the same question in the future won't find the solution here.
Asking a question on the site tends to force people to formulate it clearly and give the necessary background information for it to be answered. Getting this information in chat is often painful, time-consuming and annoying.

So, I tend to ask people to post a question on the site and then come to chat to discuss it, if necessary. That seems like the best of both worlds.
Now, there is no way of bringing questions from chat to the site short of someone manually reposting them as questions. Therefore, "migrating" is not an option, sadly. All we can do is ask the user to post a question or, if we find it particularly interesting, to post the question ourselves.

I would find it frustrating to have to link internally to existing questions (and answers) in the chat discussion when questions are duplicated, so would prefer it to be acceptable to migrate well-asked/formulated questions. Perhaps these could be done as community posts to encourage community refinement of both the questions and answers.

"Migrate" is probably the wrong word, since I don't see a technical way to migrate questions from chat, but the general idea of getting them on the main site I totally back.

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Are questions about the start point for a future career in bio-informatics on topic?
I am a math undergrad student and I'm highly interested in applications of mathematics to biology, medicine and health issues. However, my knowledge about bioinformatics is very limited. I did take a course offered on coursera about genomic sequences but that's all. I scored 100% on that course because I really found the subject fascinating. So, I was thinking that maybe I could spend more time on this website and become a bio-mathematician or at least learn whether this is something I want to do as a career in future or not.
So, I searched through the tags, looking for a tag for my question but didn't find the "soft-question" tag or any tag that fit my question. So, I decided to ask a question on meta to know whether this newly-established community welcomes questions of the kind I described. :)

I don't exactly understand what kind of questions you'd be asking. Could you give a more specific example? I am afraid you might well be right and this won't be the best place for them, but I can't really tell from your description.

Questions about career choices are subjective and open for discussion, which is a format that doesn't work well for Stack Exchange. I'd recommend posting the question on the Bioinformatics subreddit.

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Are questions looking for help to find data on topic?
There are some questions1, 2 about finding data suitable for an experiment or validate a method.
Are those question on topic?
I was going to post a new one but then I thought that it might be too broad.
Aside, I thought that a specific tag find-data would be appropriate to those questions

I vote "definitely yes". Finding good datasets to learn from, to mine, to use to teach, or for many other things can be a complete nightmare. While the odds aren't terribly high that someone will be able to reply with, "here's an optimal dataset for <insert incredibly obscure topic>", if one can't ask here, then where can one?
For the record, I consider databases to be included in this, even though they'll often be comprised of information from multiple distinct datasets (this may be a distinction without a difference).


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Are electrophysiology questions on topic?
As a mod on Bio and CogSci I am faced with quite some posts that are overlapping in all three fields. In the field of Bioinformatics I see a lot of questions (relatively spoken, as the absolute number of hardcore bioinformatics questions is, well, relatively low on both sites so to speak :-) going unanswered, simply because we lack the expertise.
Now it's about electrophysiology related questions, as a recent example see How to analyse EEG files recorded from BVA?. So this specific question is on the analysis of EEG data, but I think we should gather ERP, ECoG, single-fiber recordings and what not in this realm too and try to address the global picture here.
Now I'm not talking about hardcore signal processing questions (different stack), but there are quite often questions like:

Program w gives output x, but I need output y for use in program z (data/file conversion issues);
I use program w that outputs x, but output parameter y is missing from x, where is it (OP screwed up settings and misses some output parameter)?
Or in case of the linked question, I use program w (EEGLab) and output x doesn't make sense (OP doesn't know what they are doing).

Are these sort of questions on topic and welcomed here?

My personal definition of bioinformatics has always been "any application of computers to answer biological questions". By that definition, what you're asking which essentially boils down to analyzing biological data in silico would indeed be on topic.
However, we are a very new site and our scope isn't yet as clear as it could be. Many of the young whippersnappers current crop of bioinformaticians seem to think that bioinformatics is only NGS analysis. We certainly have an over representation of NGS folks in our user base, anyway. This might mean that we will indeed become a resource primarily for NGS questions. I hope we won't since I think it would be a shame to limit our scope that way, but scope is something that grows out of community consensus so we'll just have to wait and see.
So, I would say that yes, they are on topic or, at least, they could be. This is my own personal opinion as a user, however, I am not expressing the view of the community or of the moderation team. But I would say bring them over and we'll see how they do. I fear most of them will probably not get useful answers but only because we don't have many users who're experts in that field. Still worth a try though.

That's awesome terdon. The thing is that this type of question won't be answered over at CogSci; we lack the expertise in that arena. I could migrate that type of question to Bio, but I doubt it will be received warmly over there. I know it would be better off here for sure. I promise the numbers are not so big so we won't be blemishing your nice and shiny %answered site stat ;-) Btw - congratz with your mod-ship here!!

@AliceD you're welcome and right back at'cha :). I want to stress though that this is just my own opinion and not What The Mods Say® or anything. So the community might well decide that they're off topic. Still, we won't know unless we try. In any case, format conversion questions are often simple text parsing issues and those are explicitly on topic. So those, at least, should do fine here.

I understand it may be not everyone's pov. That's why I was a little hesitant to accept the answer up until the point I saw that shiny diamond >__<

whippersnappers?? haha  O.O


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Are (brain) imaging signal processing questions on topic?
So as an example, here 's a brain imaging signal processing question on CogSci. Although this question is well-prepared and on topic there, it will very likely never receive an answer.
This type of question also appears sometimes at Bio.SE.
Now I'd like to migrate the linked question, and perhaps others too if applicable.
Are signal processing questions on imaging on topic and welcomed here?

tldr: At present, such questions are probably less likely to get answered here than where they are.
I would have thought you'd have more cog. neuro. folks on CogSci than we would here (I'm one of the few neuroscientists here). While I think one could argue that biological image and signal processing questions fall under the purview of bioinformatics, in practice I don't foresee anyone on the site currently being familiar enough with the topics to offer any real help. Most of the time bioinfo is an umbrella term for NGS, microarray, proteomics and (sometimes) structure. So while I don't personally think such posts are strictly off-topic, I also don't think it's worth migrating them. I hope for this to change in the future as the site's user-base increases.
Update: See also this meta question from earlier. Maybe if we make this site a hub for such questions we can encourage those communities to join. I would certainly welcome that.

Thanks I'll leave them where they are then. Cheers.

Bioinformatics is just as much things like comparative genomics, phylogenetics etc. I'm always surprised when I encounter people who think of it as being essentially the four things you mentioned.

Yeah, I'm all for encouraging the broader field to participate. We NGS folks just overwhelm everyone else with our shear numbers.


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What do you think about a tag for meta discussion about the state of the profession?
I was searching for a tag earlier to add to my question here:
What happens if a major bug is discovered in a bioinformatic package that has been used in published literature?
I wasn't really able to find anything appropriate, the closest that was suggested was software-quality.
It seems to me that this stack exchange is very much implementation driven - i.e. it's more closely related to programming / software specifically.
The most common questions seem to be of the general format "How do I do X", "What's the most efficient way to do Y" etc, with the most popular tags being (predictably): R, rna-seq
 and python
I'd be hesistant to suggest the tag "meta" given it's implication on stackexchange generally, but I'm not sure what else / if anything would be appropriate.

Maybe just discussion.
Having said that, this site is really not intended for open-ended questions where there's going to be debate back and forth. The whole stackexchange network is really intended to be Q&A only. As your question regarding bugs shows, sometimes more open-ended questions can be shoe-horned into quite nicely fitting the site's structure. Other times I foresee them just getting closed, which, while understandable, is nonetheless often unfortunate.

You're probably right. I do think even though it's not intended to be for open ended discussion, often questions will provoke such a thing and it will be fleshed out over answers and responses. Perhaps I just need to think more carefully about how to word a question specifically to provoke a discussion I'm interested in.


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Are questions about analyzing and/or processing human/disease data on topic?
I'm tasked with obtaining some data about chronic disease on an human population. One of these is to identify people with a chronic disease from the data set. Since chronic diseases definition varies somewhat, I'm attempting to use ICD codes to separate those with a chronic conditions from those that do not. Would be asking which group of codes should be safely used an on topic question? Would questions about general diseases analysis on human populations?

I think Devon did a good job answering below, but I wanted to add that if the main question boils down to "is this a chronic illness?" you might have better luck on [biology.se]. If you think you can ask the question in a way that fits the SE model (so if the list is not too huge, I guess, but you know the model better than most, I'll let you decide), you could try there instead.

I think asking about mining databases using ICD codes could be on-topic. Having said that, I don't perceive much in the way of community knowledge surrounding that at the moment (perhaps I'll be pleasantly surprised though!), so I'm somewhat pessimistic regarding how much help you'll receive.
Asking which codes are best associated with which disorder is getting fairly off-topic, since that's moving quickly into the realm of the clinician (after all, you end up needing to know a bit about the local billing practices and disease prevalence to be able to judge whether the labeled ICD codes really do correspond to the appropriate condition).
"General human disease analysis" is largely going to be off-topic unless it specifically references a bioinformatic technique or method. Much of that will be standard wet-lab sorts of things, which will be quite off-topic here.


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Closing because a question is cross posted?
A question has been closed as off-topic, and the moderator who closed said in a comment:

This is already receiving sufficient attention on biostars. Giving it further attention here would be a waste of community effort. Consequently I'm closing it.

I have seen comments about cross posting with biostar and other sites. But I don't think that makes a valid reason to close the question here. Many questions in stackexchange.com are duplicated between sites (specially those about ubuntu and *UNIX)
Highly relevant, stop cross posting petition doesn't seem to work. What should we do with those cross posted questions?
My personal opinion is that closing them because is off-topic is not right. I would let them open, but maybe it is time for a custom close reason?

We don't seem to have a consensus!!

I'm tending to agree with terdon, but it may be useful to distinguish between cross-posting on SE sites to cross-posting on other sites, the former can be dealt with by different mechanisms (e.g. question migration, although in practise this rarely occurs)

@Chris_Rands At the moment with so few question I don't think we have to deal with much cross-posting within SE, my question was more addressed to cross-posting with biostars, and support.bioconductor.org, seqanswers...

Well I have seen cross-posts on Stack Overflow, but I agree it's probably not the main cross-posting source; anyway, there will always be redundancy on the internet (and that's not a bad thing) so as long as there is no plagiarism I have no issue...but I'm not a member of other sites like BioStars and I can see why people active on both would get frustrated, nonetheless, anyone wanting a quick answer is going to cross-post inevitably...

My personal opinion on this (which is not that of the moderation team), is that we should leave them alone and just try to answer them. I really don't understand this insistance that someone should ask on our corner of the internet and nowhere else.
Now, I do agree that it would be very nice of the OP if they were to link the two and repeat any answer given on one on the other, but surely the main objectives here are i) to share knowledge and ii) to get answers to questions. Both of those objectives seem to me to be served perfectly well by cross posting.
Do we really want to close a question just because the OP didn't choose us over BioStars or vice versa? We're a very small site still and the volume of posts we get is tiny. If we tell people that in order to ask here they must ask here and nowhere else but here, the chances are we'd just drive them away to the more populous communities where they'll feel they have a greater chance of having their question answered.
If a question asked here already has a great answer on BioStars, we should just copy the answer here—giving credit to the original author, of course—and link back to the original answer. Even better, we can read the answer given, add our own two cents and post a new, better answer here.
But if we decide that any question that has been asked elsewhere cannot be asked here, we deprive the site of a wealth of useful information. I think it is important to build a good collection of interesting and helpful Q&As here, and removing good questions just because they have been asked elsewhere is directly against that goal.

I would support making a custom close reason. If the post isn't yet sufficiently answered on the other site then leaving it opening and posting a link to the other post is the best course. However, if the post is sufficiently answered elsewhere then any effort spent here is a complete waste of time, in my opinion. We use the same strategy on biostars, for whatever that's worth.
Update: I've created a custom close reason, it just needs to be approved by one of the other mods.

I admit I am strongly against such a custom reason. We have one over on [unix.se] and I've never understood why. I really don't see why someone should be forced to ask in one place and one place only. It is never a waste of time to put information out there. You never know which site a user will be searching on, and you can always repeat whatever information on the other site.

I don't innately have a problem with asking multiple places (provided you link to them), the question really becomes whether it makes sense to ask different people to provide what will in essence be the same information rephrased multiple times. As long as the answers elsewhere are linked to, a user will be able to get to the information conveniently where ever they happen to be searching.

Its pretty annoying to waste half an hour of your life, only to find that a question has a perfectly good answer on a different site. Often I think this happens when a questioner doesn't get the answer they want somewhere else (i've done this myself). Sometimes the answer elsewhere IS wrong. But sometimes the questioner just doesn't want to hear the truth.

@IanSudbery why would that be an hour wasted? You have just written up a nice answer to an interesting question, thereby increasing the amount of useful information found on the site. How is that a waste of your time? We don't answer questions (just) for the person who asked them, we answer them to build a repository of useful information.

The amount of information on the site has increased, but the amount of info on the internet hasn't. There is some value in that, but not as much as answering a question for which there is no good answer around (given I only have time to answer one question). I should good the title first to check. But if we all do this we (and other sites) will end up with a lot of unanswered questions when people decide to put there effort where it makes the most difference. Of course if the answers on the other site aren't good, that's different.


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Community promotion ads
Shall we start a small advertising campaign?
Some Stack Exchange communities vote on “community ads” — banners that link to other resources related to the topic. Highly voted proposals get free ad display time on that community. Here’s an example for an ad for the “Genealogy SE (beta) that’s displayed on the Biology.SE site.
I suggest creating a similar banner for out budding Bioinformatics site and suggesting it on some Stack Exchange sites — for example, Biology, Stats, Chemistry (?) etc. (Unfortunately not all sites have community ads, and in particular Stack Overflow doesn’t.)
For this, we will need:

A banner design
A tagline (to be displayed on mouseover)

Yesh! Great idea! I hope someone else can come up with a nice banner. If not, I'll do it but given my complete lack of any talent in that respect, I'd really prefer if someone else could.

Great idea, can you add a ss of that ad?

Nice idea, I also think anything tagged with 'bioinformatics' on SO could potentially be directed towards here, even if just via a comment

Unfortunately I’m (a) not a graphic designer, and (b) short of time at the moment (too many projects at once). Unfortunately it doesn’t seem as if anybody else is up for creating a banner.

Are you all still interested in doing something like this? I'm pretty handy with Illustrator and could try to put something together.

@Geraldine_VdAuwera Absolutely, that would be great. I’m currently not very active in online communities due to other commitments, but I’ll happily upvote and promote community ad designs.

Alright I was playing around and made this nerdy old-school graphic which I'm embarrassed to share, but maybe it can serve as a conversation starter to figure out what direction we want to take on this.

I’m not sure about the tag line, but I do like pretty much all of the rest. However, I just noticed that the last “community ads” activity from Stack Exchange was in 2013, and I’m now wondering whether that programme actually still exists.

OK, community ads are still active!

That's a relief :)
Yeah I agree the corny tagline is meh.

Exciting.
I think if @KonradRudophs advice is followed this is a positive step toward 'lift off', i.e. moving out of beta version. The site has been on 5 questions per day for some time now (minimum threshold for 'lift off') and this seems to be a function of the total number of views per day which is now around 2K to a maximum of 2.5K per day. As a whole the traffic here is increasing and promotion can only help.
@GeraldineVdAuwera graphic looks fine, thank you, and good enough for a  banner. It could always be upgraded modified later. I wouldn't worry about the polish at present, considering we're essentially 'backend developers' rather than 'frontend designers'.
Could the 'icon' for bioinfo.SE be upgraded?

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Should pure statistics questions be on topic?
This question was prompted by differential gene expression complex design no replicates.
While that question isn't very clear, it seems to be essentially asking for help on applying statistical methods to get a result. It isn't asking for help on a bioinformatics method, but for help on choosing the right statistical approach to analyze the results of a wet-lab experiment (RNAseq). If this were asking for bioinformatics methods for analyzing RNAseq data, that would be fine, of course, but if the OP is requesting for help on choosing the right statistical approach, do we consider that on topic?
Note that if the answer requires you to understand the underlying biology, then of course it should be on topic. I am thinking of situations where the details of the dataset are irrelevant and the question is one of pure stats which could be aplicable to any field.

I generally agree with @Ian Sudbery, but I would phrase this as I would prefer that the site's purview be "anything an expert bioinformatician might reasonably know that has at least a tangential relationship to bioinformatics". This would include statistics, biology, and some more general CS related questions provided they have some clear relationship to bioinformatics.
I should note that this makes it exactly the same as biostars, the scope of which some people don't like.

My feeling about the distinction about here and biostars is that biostars is explicitly aimed at beginners, where as I feel it would be useful if this could be a place where experts found it useful to ask questions as well as answering them. Questions where the answers wouldn't be completely obvious to anyone who had been in bioinformatics for a while, but required properly specialised knowledge about a sub-area, weather that was the stats of an unusual datatype, how to implement a particular algorithm efficiently, or a genome annotation feature particular to a specific species/assembly.

I think the scope of biostar is good. It is the other things that concern me more.

I'm not sure how explicitly biostars is aimed at beginners, but it's certainly become that way.

@IanSudbery ideally, we should be able to do both. I mean both help experts and help novices. I don't see the two as mutually exclusive.

DevonRyan: I'm sure I'd seen that somewhere, can't find it now though. @terdon absolutely, I'm just commenting on the idea that also supporting experts could be something that distinguishes us from biostars (even if biostars not supporting experts is by accident rather than design).

I think stats if very much on-topic. If we want the site to be useful for experts to ask questions and get informed answers from other experts, rather than a site where newbies are just instructed on how to install a piece of software, or where to find the limma manual, how to convert one file format or one gene id format to another (and other sites already fill this niche, then I think many of these will effectively be stats questions.
There is already an SE site dedicated to statistics, but in my experience questions that are about the stastics of bioinformatics rarely get helpful answers there. Partly I believe that this is because by the time you've explained the requisite bio background to understand the question, people have switched off. Here we get better engagement.
For example, I asked effectively the same question on here and on cross-validated.. After nearly 2 years the cross-validated answer has no useful responses, while the one here got answers very quickly.
Of course this is probably related to how you view bioinformatics, which I basically regard as a branch of applied statistics these days.

I am thinking about situations where the bio part of the question is irrelevant. if you need to understand the underlying biology to be able to answer the question, then it belongs here. No argument there. If, however, the biology is irrelevant and the question is one of pure stats, then I think it belongs elsewhere. I'll try and edit my question to make that distinction clearer. That said, I personally view bioinformatics as theoretical biology and absolutely not as statistics. Of course, that's because my background is in biology.

Take a look at my questions linked - its basically pure stats (how do a characterise the relationship between two spatially resolve count variable with high amounts of missing data). But unless you can explain why you are trying to do that, you don't get any answer other than "why on earth would anyone want to do that".
What is theoretical biology other than mechanistic modelling (which I grant isn't stats) and statistical modelling.

I'd say your question is on topic, yes. But that's because it is about a particular type of data whose characteristics you need to know in order to deal with it. In other words, a typical example of a case where you need to understand the underlying biology in order to provide an answer. Note that the answer you got is basically "use these standard bioinformatics tools" and not "use this stats method". (I won't answer the "what is bioinformatics" question here since it would derail the discussion; happy to chat about it though!)

Most of the answers did suggest using existing tools, but I didn't find those answers useful, there were generally answering a different (but related) question.The two most useful answers were the second half of CloudyGloudy's answer and Sasha Favorov which pointed to a preprint dealing with the same problem (which is a very stats heavy paper).

Well, my main point is that any answer you receive would require a relatively deep understanding of the kind of data you have and therefore your question isn't purely about statistics. Have a look at the one I cite in my  question. That looks like it can be answered by any statistician. There's no need to know about RNAseq, it's essentially an issue of comparing data points.

I left an answer for the question you referenced just before I saw your post here. I'm not sure its true that any statistician could answer it. You'd need to know, for example, that RNA-seq data is negatively binomially distributed, that log TPM can in some cases be estimated by a normal, that the model is likely to need to be fit to many thousands of genes...

Fair enough. That might not be the best example then. But do you feel that questions that can be answered by any statistician without needing to udnerstand the details of the experimental method used should be on topic?

Sure, if someone came on and asked "How do I carry out a t-test?" or "how do I use R to fit a normal linear model" then that absolutely wouldn't be on-topic.

Yes, those are the types of question I am thinking of. I tried to make that clearer with my edit: "Note that if the answer requires you to understand the underlying biology, then of course it should be on topic. I am thinking of situations where the details of the dataset are irrelevant and the question is one of pure stats which could be aplicable to any field."

Okay, sure. I'm interested though why your response to this question is different to your answer to "How do we feel about questions that are essentially about text parsing?"

Ha! Um. shuffles feet. Probably because I hate stats and enjoy text parsing. Which is an absolutely crappy excuse. But you make a very good point, it doesn't make sense to treat the two differently.

I just revisited this. I think the community is clearly in favor of stats questions, and your last comment showed up my own obvious hypocricy given how I feel about text parsing. I guess my initial position was based more on my ignorance and visceral fear of stats (I'm a biologist at heart) than on any real scientific reason. So I accepted Devon's answer since it was the most upvoted.

Just to chip in, I'm strongly in favour of stats questions being fine given a biological context because they'll be a bioinformatics solution somewhere.
Modern bioinformatics appears to have become removed from its "statistically pure" origins but it moves cycles. At present many think (perhaps correctly at present) the volume of genomics data renders "the statistical model" irrelevant, but things change. When "the statistical model" is king, the reality is the method was shoe-horned from another area of stats/maths. The "shoe-horning" process is quite important, because your trying to place a generic solution into a biological context and the translation isn't always neat.
Example 1
For example, we just had a question asking whether "clustering analysis" can replace molecular phylogeny ... the answer is no and this question was asked about 40 years ago. However, a general statistician wouldn't be aware of the biological rational as to why, nor aware of the huge row broke out in evolution about "the correct method to build a phylogeny" and took a decade to resolve.
Example 2
A good example of "statistical methodological cycles" is machine learning (ML), which is currently fashionable, but has been on the go since the '50s. Purists describe "AI winters" (sounds like Game of Thrones, but before GoT). This is where funders pull out because the original PIs overstated their case. Without AI winters its application to bioinformatics would be much more mainstream (possibly). The reality is that many major genomics packages Sauret (whatever its called), don't implement "full-blooded" ML solution, so there's lots of ground for change.
Example 3
Finally an older but brilliant example (brilliant man) of the importance of empirical statistics specifically applied to bioinformatics was Ron Fisher's F-statistics (e.g. Fst). Fisher was a statistical purist who founded large chunks of modern statistical theory, but also applied that expertise to biological questions (just don't ask about his political views). F-statistics are used in vast numbers of bioinformatics packages and population genomics including R and I've no doubt they'll be a BioPython solution somewhere.
My advice "resist popularism" :-)

I would say that questions that are asking for help on statistics and nothing else should not be on topic. While statistics are an integral tool of a bioinformatician, they are not really part of bioinformatics. They're an integral tool of any quantitative science.
There is already an SE site dedicated to statistics, and I feel such questions would be better served there.
Note that I am not advocating that any mention of stats would make the question off topic, only that if the question is just asking for statistics help, it doesn't belong here.


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Where are the bioinformatics questions in other SE sites? (Community wiki)
Subject: This page is specified for discussion for feature development to  link this site  with other sites those too containing bioinformatics question.
Related: should we import questions from other SE sites?
There are many other sites within Stackexchange Network that contains bioinformatics question. Some could not be transferred by design because they crossed 60 day age, and for the other question there may exist some-other problem, so universal migration could be impossible.  to filter all bioinformatics question
But as an alternative solution to migration,  if we want to easily browse/filter those relevant (since they are  bioinformatics questions) while using only bioinformatics SE, it would become
 useful; and (and also it would not be any harmful except it is going to take this 1 page only!).
As a self-answered article I (@alwaysconfused)'ve tried to copy-paste some quick-links from search-filters. But other users can improve it or post their
 work as separate answers.
How other users can improve/ contribute?

Other users may implement better commands to give the link a shape of button,
or may add a preview window, or may add more search-filters,
or may also help build techniques or principles to track question on other sites that don't directly tagged as bioinformatics but actually are bioinformatics questions.
Any other views welcome.

I think, beside ease of browse/filter;  some other advantage we'll obtain are;

more exchange of thoughts  between separate streams (so reduced tunnel vision). It will help find correlation between separated streams.
Would also help to find duplicate questions, related questions, etc.

I don't understand the question: Do you want to know where are other bioinformatic questions in order to propose to migrate from x site to Bioinformatics. Or just to have a list of sites with questions related to bioinformatics

No. Not to propose migration but just to easily find/ filter at one place @Llopis

But what do you want to "find" at those places? What do you want to filter at those places? That doesn't affect the community here (although we might be interested in answering those questions)

@Llopis You confessed, "although we might be interested in answering those questions". Yes, the linkup would promote the users of this-page to visit bioinformatics questions to other pages, and could share their views.

Also we don't browse question only for answering. We browse question for learning, isn't? so a filter must help in learning.

When I want to learn how to to X I search for X, I don't go to a page with links to informations to X,Y, and Z. Wouldn't be of more interest for people on those sites to come here on this site to ask?

Yes, and indeed a discussion is going on BioSE. Good point, but older question (those couldn't be migrated); are already have been asked; bioinformatics SE didnot born then. so to view them we might need a shortcut.

@Llopis and it would really be good if bioinformatics questions specifically asked at this site, but even after birth of this site, many bioinformatics question asked (submitted) in other SE sites, maybe many users still do not know about/ not used-to with  this site, or maybe they want a more biology/computer/other field oriented expertise. Still, if users of this-site could easily found them, (and so ways for exchange of thoughts are broadened) , it would be nice.

One simple way is to comment in all questions of each site to raise awareness of this site. Specially if someone is active in other sites

I already mentioned it in a discussion at BioSE. I can't alone make an action in a community, I can only express my-views. Everything else now depends on other users.

You can edit the tag, to try to redirect users, or at least let them know each time they use the tag

Let us continue this discussion in chat.

I also don't understand what you are suggesting here. Could you please [edit] your question and explain what your suggestion is? What does any of this have to do with the site's scope? What are you asking about (if you're asking anything)?

Also, are you just looking for https://stackexchange.com/filters/ ? You can set a tag there and it will return all questions tagged with that tag from all sites of the SE network.

Here is a list with links to the bioinformatics tag in other sites in the Stack Exchange network:

Biology
site
Cross validated
site
Computer science
site
Stack Overflow
site


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Are questions about installing bioinformatics tools on topic?
Should we allow questions asking for help installing specific tools? Some of the tools that are commonly used in bionformatics are non-trivial to install. They can require other packages, environment variables etc.
On the one hand, the programs are indeed specific to bioinformatics, on the other hand, the issues faced when installing them could be applicable to pretty much any program distributed in similar ways.
So, what do we do? Is "I am trying to install GATK and get this error" a valid topic for us? Should we send them to existing tech support sites of the SE network, or do we keep them here?

Just a reminder that some tools don't have support sites, and the support (if any) is contacting with the authors of the tools

@Llopis I was referring to other sites on the Stack Exchange network where software installation issues are on topic. Places like [su], [unix.se], [apple.se], [ubuntu.se] etc. I edited to clarify.

I vote yes, since I totally agree that some of these are a real nightmare to install (I'm not laying blame, I'm also responsible for this). As always, as certain amount of, "Here's what I've tried" should be expected. At least if we answer these here they'll be picked up by search engines, the same can't always be said for other random forums.

I would say yes, too.

As is frequently emphasized on other stacks, because something is on-topic in another stack is not a reason it has to be off-topic on this stack. In this case, on-topic here seems fine.

I'd go with on-topic for such questions, and hold them to the same standard requirements as they would be on Super User, etc. If, as originally posted, the question is of low quality, the community can help the OP refine it (perhaps using chat) so that it becomes a quality question.
Would this be the best place to ask such a question, even if on-topic? If the installation has some twist that makes it a problem unique to the field, then it's probable that users on SU, et al., might not be of much help. OTOH, if the "problem" is common to many other package installs, the needed help might be best found on the other stacks anyway.
From a community stand point, if a package is commonly utilized in the field, whether or not it's also common outside the field, and frequently has tricky issues to get it installed, the question, and eventual answer, will benefit the community, and likely increase its search engine exposure as well. The trade off is that the OP might have to wait longer to get a useful answer to the problem if asked here, rather than on a larger stack.


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[alignment], [sequence-alignment], [read-alignment] and [msa] tags
Let's decide here on the status for different tags related to alignment.
There are two groups of questions.

One is related to pairwise and multiple sequence alignments and algorithms. This field is definitely old and it was one of the keystones in the bioinformatics development. You get question like alignment tools supporting codons, RNA alignments editing or full genome alignments.
Another one is related to read alignment/mapping. We mostly get mapping software related questions like obtaining uniquely mapped reads, BWA-MEM scoring or  building genome index.

Of course read alignment is a series sequence alignment steps. In practice, however, most of the current [alignment] questions are specific only to read mapping software, and has nothing to do with sequence alignment methods.
I think we need to think about tags pragmatically, it is a way for people to follow what they are interested in, and clearly these two areas are of interest for different people. In that line, it is worth noting that meta-tags are considered useless and should be avoided.

If the tag can’t work as the only tag on a question, it’s probably a meta-tag
If the tag commonly means different things to different people, it’s probably a meta-tag

These are the results from our quite diverse lab, where some people are working with RNA-seq data. Clearly just [alignment] is ambiguous.
In the current form [alignment] is a meta-tag.
Meta-tagging is explicitly discouraged.
I see two ways of dealing with this.
Two separate tags
For the read alignment I propose using [read-alignment] tag. It's unambiguous.  Using [alignment] wouldn't be fair because a) sequence alignment preceded read alignment b) some people (including me) still think about sequence alignment by default c) if you search google scholar for "alignment", four out of five top results will be related to sequence alignment.
For the sequence alignment I propose [sequence-alignment]. I wouldn't use [alignment] for the same reason as above (it's ambiguous). [msa] is a poor choice, since msa is considered to be an extension of pair-wise alignment.
Use [alignment] only for the sequence alignment
In this case we have to remove the [alignment] tag from all the read-mapping questions, where the alignment itself is not a problem. Maybe replacing it with [read-mapping] in some cases.
What are your suggestions?
P.S. It goes without saying, that a question related to both read alignment and sequence alignment could be tagged with the both tags. E.g. "Is it practical to use Smith–Waterman algorithm inside XYZ-mapper".

Please don't downvote this question if you disagree with the proposal. The question is basically asking what to do. If you feel that keeping a single tag and keeping it named alignment is the right option, then downvote my answer, not the question.

I am folding my previous answer, EDIT and comments into this new answer.

sequence-alignment includes read alignment. This is both conceptually and practically correct. The most widely used read alignment format is SAM, which is an acronym of "Sequence Alignment/Map" format. i.e. SAM is a sequence alignment format. This naming was unanimously approved by the 1000g committee consisting of many top experts in the field. Having worked with various sequence alignments for many years, I simply can't accept we exclude read alignment from sequence alignment.
The biggest problem with sequence-alignment is that it means different things to different people. Those in phylogenetics may think it means traditional alignment exclusively. Those who have only worked with NGS data naturally think of read alignment. In fact, this tag includes both fields. Forcing this tag to only mean traditional alignment is a wrong thing we should stop populating. It will also lead to confusion to NGS people.
A meta tag is an excessively broad or excessively ambiguous tag. Telling excessive broadness and ambiguity is sometimes subjective. An obvious meta tag (e.g. "best practice") can be put on almost all questions without narrowing the questions down to a specific field. Currently, we have two less obvious meta tags text and reference due to excessive ambiguity. text does not represent a field in bioinformatics. It could mean text mining or text processing, two distinct fields. Similarly reference could mean reference genome (I have retagged all questions taking this meaning) or literature, again two distinct topics. Importantly, a tag is not necessarily meta if it can be divided to more specific subfields. Actually, a true meta tag often can't be subdivided because it lacks a clear scope.
To me, alignment is not meta because it clearly defines a subfield in bioinformatics. If we think "alignment" is meta, "read-alignment" would be meta, too, because it includes both DNA read alignment and RNA read alignment. I can't just follow read-alignment if I am only interested in RNA-seq. In addition, alignment is frequently a safe fallback tag when the asker is not familiar with the different types of alignment. I predict it would keep popping up with time even if we retagged all current questions.
I don't think there is a right terminology for "alignments that are not read alignment" because each other type of alignment belongs to its own field and often uses distinct algorithms (at least partly). I think at the current stage, the best we can do is to create a tag for a smaller category of "traditional alignment". I propose to use "msa" (with "multiple-sequence-alignment" being a synonym) for MSA, "rna-structure-alignment" for RNA structure-aware alignment and "full-genome-alignment" for genome-vs-genome or assembly-vs-genome alignment.

Conceptually bioinformatics is biology, and why do we need a separate SE? :)
From the practical point of view, I suggest you check the questions. They are conceptually very different and most of current [alignment] question have nothing to do with the sequence alignment itself.
Also, I explain why msa is not a good choice of tag. Otherwise we should have another one for pairwise alignment, which sounds too specific.

In any case, [alignment] in a current form is a meta-tag. We should do something about it; and introducing msa doesn't solve the problem.

Yes, but not to everyone and tags should be understandable in the same way by everyone irrespective of their subfield. So since alignment can and does mean different things to different people, it isn't a good tag. You are an expert in the field, so of course you understand that read alignment and sequence alignment are essentially the same thing. Others, however, can be confused by this. Plus, the word is so ambiguous that I'm willing to bet we'll end up having people tagging questions about left-aligning variants or even printf output with alignment.

@user172818 I agree completely that [alignment] is a correct term. But it doesn't make it a useful tag (e.g. I would probably subscribe to [sequence-alignment], but not to [read-alignment]). I know that you have a proficient experience in both, but it doesn't mean everyone does; you can subscribe to both. And again, when read-alignment problem is really boils down to sequence alignment, one can use both tags. Tags are not about ontology, it's about filtering the content. Could you have a look at the blog post on meta-tags?

@user172818 There are two separate issues here: i) whether we should have separate tags for "traditional" sequence alignment and short read alignment and ii) what should those tags be. My main issue here and, I think, Iakov's, is that we need separate tags for the two. What that tag should be is debatable but I feel very strongly that we need to have different tags for these two types of alignment. Now, using sequence-alignment and read-alignment seems the most natural and obvious to me. That doesn't in any way suggest that read alignment is not a form of sequence alignment!

[cont] Of course reads are sequences and aligning them is a form of "sequence alignment". But that's not what most people would think of when they hear the term "sequence alignment", I think. Most of us would think of Clustal & co and not BWA & co. But we could have another wording if you like. As long as we have two separate tags for it.

As for alignment by itself, that is a meta tag. The definition is not subjective at all: it is a tag that, by itself, does not define what the question is about and needs a second tag for clarification. "Alignment" is ambiguous. It can refer to aligning NGS reads, whole genomes, proteins, genes, RNA, structural alignments, left-aligning variants. . . And it has meanings outside jargon, in everyday language as well. This is not a good tag.

@user172818 then let's use different names! All I am really arguing in favor of is to not have a single tag describing "traditional" sequence alignment and NGS-style aligning of reads to a genome. If your objection is only to using the tag sequence-alignment only for the former, then let's use another name for it. How about multiple-sequence-alignment and read-alignment? I would argue against genome-alignment since that could be for aligning genomes, and against msa since that's not very descriptive.

I agree with this. To me the word alignment will always mean aligning sequences to each other and not aligning reads to a genome. Yes, the two are not really different under the hood, but that's not the point. Tags serve two main uses:

They make it easier to search for topics;
They help experts find questions they are interested in (through marking a tag as a favorite).

Although the underlying methods involved in both multiple sequence alignments and read mapping are not fundamentally different, the tools used for each are. Also, the people interested in each and knowledgeable about each are not always the same. I, for example, am far more familiar with sequence alignment than with aligning reads.
So, given that we have two sets of not necessarily overlapping experts and two different subjects, having two tags makes sense. The tags should serve to clearly mark what a question is about. Tagging something with alignment is not really informative since we don't know what kind of alignment we are referring to. In general, I am in favor of making tags be as descriptive and unambiguous as possible.
I would therefore be in favor of using sequence-alignment for multiple sequence alignments using tools like t_coffee of MAFFT and read-alignment for tools like bwa or bowtie that align reads to a reference. We should then remove the alignment tag since it isn't enough to explain what a question is about by itself.

I don't see an easy distinction between sequence-alignment and read-alignment. It could perhaps be argued that if someone is mapping and aligning lots of reads to a genomic reference, then that's read-mapping, and if alignment is not being done at the same time (e.g. Kallisto, Salmon), then that's quasi-mapping or pseudo-alignment.


text:
Moderator Pro Tem Announcement
Throughout the beta, we need members from the site whose focus is to engage the community, both in community-building issues and site management. That's why we select a few members from each community to act as temporary, provisional Moderators. You can read about the program here: Moderators Pro Tempore.
I am pleased to announce that these members have stepped up and generously volunteered their time to help us assure that each community’s issues are properly addressed.

We want to make this site a huge success, and these members are great examples of exactly the type of people we need to make this site succeed. Please welcome them for the hard work and time they contribute.
Did I overlook anyone?
Almost certainly. There are members who are actively involved and very deserving of recognition. My failure to account for everyone this early on is in no way a slight against them. Ideally, Moderators are elected by the community and that's why you'll have your elections once your site has graduated.
Most of all, be respectful and understanding of the Moderators Pro Tem. Members of your community are volunteering their time and learning on the job. It’s a learning experience for everyone.

Congrats to the new Pro Tempore Moderators! Let's hope you don't have to use your powers as moderators but help to built a great community.


text:
Q&A-style answering bug where "40mins between questions" hidden by answer box
When posting a Q&A question, the warning that you can't post within 40mins of previous post is hidden by the "answer" portion of submission.  When the answer section is there (i.e. the box has been ticked) and a post is submitted, the page refreshes with seemingly no error message.  Once I unticked the "answer own question" tick box, the error message about rapid posting came up.
Ironically, I can also not post the bug report here, until 40 mins is up ;).


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Should we be asking OPs to accept answers?
I have been seeing a lot of questions on here with answers, but most don't seem to have accepted answers (the check mark thing next to the answer comment). Based on my (limited) experience with SO, this is important for closing a question as being answered. Should we be flagging the answered questions to be accepted? Thanks! :)

"closing a question as being answered": Questions are not "closed" after an answer has been accepted. It continues to be possible to update answers or to post new answers, and the OP can change what answer he/she "accepts".

Actually, it isn't very important at all. All it takes for a question to be marked as "answered" is either an accepted answer or one answer with a positive score. So just upvoting an answer is enough to mark the question as answered.
Also, accepting simply means that this was the OP's personal favorite answer. It doesn't indicate the best answer, or the simplest or the most beautiful. It's just the OP's choice.
That said, on the sites I'm active on, I tend to leave a comment like this when I see the OP leaving thank you comments:

If this answer solved your issue, please take a moment and accept it by clicking on the check mark to the left. That will mark the question as answered and is the way thanks are expressed on the Stack Exchange sites.

I try to only leave such comments when the OP has commented on an answer. The objective isn't to badger the OP into accepting an answer, it is simply to point out that instead of leaving thank you comments which are just noise and clutter up the site, they should accept the answer and that's how thanks are expressed here.
So, I would say that if the OP has not given any indication that they've read an answer, asking them to accept is pointless and pushy. If, however, they seem to have appreciated an answer and yet haven't accepted, then maybe they don't know how the system works and we should leave a comment like the above to inform them.

Please don't prod users into accepting answers.  The system already prompts users to accept an answer at an appropriate time, but accepting an answer is a completely voluntary activity, and it is up to the user to decide when (and if) they choose to accept an answer at all.
Such comments might seem like a  harmless reminder of a feature a user may simply have forgotten, but the folks looking on will imitate what they see… so as the sites start to fill with "please accept an answer" , "can you accept my answer?" … it starts to become somewhat noisy and annoying (and even a bit harassing) to just about everyone else looking on.

I haven't seent this prompt in a long time so I don't remember how it works. However, I've often seen OPs post thank you comments and, after being prompted to accept instead of thank, they do accept so maybe the prompt isn't always shown?


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Should we allow questions where the title is not a question?
I think there are too many entries where the title is not a question.
Related discussions:
How do I write a good title?
Should question titles be phrased as questions? (A straw poll)

There's no reason to require that titles be questions. That's just going to make them longer than always needed.

OK. I was under the impression that titles had to be questions, but apparently that's not the case.

I very much prefer titles to be a fully formed question, yes. However, requiring it goes a little too far, I think. I also disagree to some extent with the related discussion “How do I write a good question title?”, which exemplifies my grievance: I believe that, contrary to what answers there claim, starting a title with “How do I …” is not only OK but actually desirable: it focuses the subsequent discussion. “fooing the bar” invites so much more discussion than “How do I foo the bar?” in my experience.
For context, I’m often editing unclear question titles on Stack Overflow, and 90% of the time1 the title becomes much clearer when phrased as a question.

1 Admittedly I just made that number up. But it feels right.

I take your point, but where this is a problem, it's more that the "question" isn't a question or doesn't make clear what the exact question is. The title is just a symptom.
Looking at it another way, there are many suitable titles that aren't strictly questions (e.g. "Limitations of single molecule sequencing", "Searching for gene expression data by cell line", "Visualisation of long read RNA-Seq splicing"). Insisting on a strict form is wasted effort.

Thanks, yes I agree.


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Should [benchmarking] and [performance] tags be synonyms?
I just created a "performance" tag for this question.
I went to see if this tag could be added to other questions, and thought about this one, that happens to already have a "benchmarking" tag.
Should those two tags be synonyms?

benchmarking largely means evaluation by comparisons. performance does not imply comparisons. In addition, benchmarking evaluates accuracy in addition to performance, I think. They are not synonyms.


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What do we do with [software-recommendation]?
software-recommendation seems like a highly questionable tag to me, yet it’s collecting questions.
On other Stack Exchange sites, most notably Stack Overflow, software recommendations are explicitly banned, since they age badly, admit more than one right answer (opinion based), etc.
I can see the appeal of such questions but I think we should decide as a community how we deal with them.

Allow software-recommendation questions
As mentioned in the question, I do see the appeal. And just because Stack Overflow banned them doesn’t mean we have to follow the same hard line. There are certainly both pros and cons to allowing them, and maybe Stack Overflow actually got it wrong, and the pros outweigh the cons?

I voted for this one, mostly for cases of "I need to do X and I've tried tools Y and Z. Neither of those suffice because of reason W. Are there any other tools that do X while avoiding W...". Certainly the pure "give me a list of tools for X" should be discouraged, that's what google is for.

@DevonR Yes, a pure list of software names is discouraged, but a list of tools with reviews and discussions is encouraged and is actually better than recommending a single tool. The best recommendation comes from those who are familiar with multiple similar tools and know their pros and cons.

Usually we do not recommend single tools but more than one tools but at the end of the day it is also the duty of the OP to check that in Google. Tbh in omictools page one will find plethora of hits for software recommendations that performs for specific functionalities. Having said that still users ask and then people with more knowledge and expertise either direct to citation based or review based article.

Something in between: allow the tag and the questions but set some guidelines. I propose the following:

Be specific. You need to clearly state your needs and the specific features this program should have. There's a great post on Software Requests Meta with their guidelines which is worth a read. Basically, they boil down to:

Explain what you want the application for. What will you be using it for and in what context.  If it is to be a replacement for something you're already using, tell us what that program is and which of its features are essential to you.
Specify what operating system the tool you are looking for should work on.
State whether you are willing to pay for it and, if so, what your budget it.
Give a clear list of specific features the application must have.

Ask for one tool, not many. Questions like "What tools are available that can do foo" are off topic since by definition, their answers will be long and unmaintainable lists. The only exception is cases where foo is something very specific as listed  in point 1. above.
Ask for a specific tool and not for people's favorite. So, instead of "What's the best tool for foo?", you should ask something like "I need to do foo (where foo is specific as described in 1.), is there any program available that can do it?".

So, as long as the questions are specific, not too broad (lists) and not opinion based, I think we should allow them.

Ban the tag, close the questions
One course of action would be to proceed like Stack Overflow, and to close such questions and ban the tag altogether. We might even be able to create an automated message along the lines “This type of questions is discouraged here” when somebody tries using the tag.

I think this would make this site miss the opportunity of very useful answers. The answers will of course age, but updates are welcome, as well as newer answers.


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Is it okay to write a post Introducing a tool?
I have just developed a new bioinformatic tool and I was simply wondering whether it is okay to write a post introducing the tool?

Yes, but only if you:

Post a question asking how to do something that your tool can serve as an answer to. This is strictly a Q&A site so everything needs to be posted as either a question or an answer.
Post an answer explaining how to install your tool, where to find it and an example that shows how to do whatever the question asked.
Clearly state that you are the author of the tool. See How not to be a spammer.


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Are we supposed to delete comments, once the issue has been resolved?
Sometimes a comment, leads to the answer (or question) update. In such case the comment is not relevant anymore, since it addresses a resolved issue.
Are we supposed to delete comments like this? E.g. here:

The second point is not fully true. <...> – Iakov Davydov

<...> I update the bullet, thanks Iakov – Llopis

What about comments like: "Thanks, I updated my answer"? If the original comment was deleted, this looks strange.
In my opinion we should remove these comments, since they are not informative. What do you think?

Yes, obsolete comments should be removed. Always. We even have a flag to clear out 'obsolete' comments that may have been missed.
Comments were included with every post for a purpose — to ask for clarifications or otherwise help improve the post. Comments are there to help facilitate the wiki-style editing in Stack Exchange that helps assure every top-voted answer contains the most complete, accurate, and current information available for that answer. Questions are improved in a similar manner.
But once comments serve that purpose, they should be removed.
We don't want to create a situation where, after every answer, the user has to pour through a series of addendums to see if the answer is actually complete… or is it the start of a meandering conversation where we swerve into the correct information at the bottom of page 18. That was one of the failures of threaded discussion forums which prompted the creation of Stack Exchange.
Once comments have served their purpose, they should be removed; otherwise, it's not clear whether the vetted answer is actually the complete answer or not.

I'm not sure people are flagging obsolete comments. As an example, a question I recently wrote is littered with obsolete comments...

Or maybe my understanding of obsolete is just wrong...


text:
Questions about commercial products where there are official support channels
Though inspired by this question, this tends to come up more often in relation to CLC Workbench. On occasion, people using commercial closed-source packages will post questions about using said tools or analysing their results. 99% of the time these products already have official support channels that the posters will have already payed for but either aren't using or have just hoped that we will respond faster (therefore performing the role of the company for free).
I personally am very much against answering such questions, since it has the perverse incentive of promoting companies not providing support for their products. Over on biostars we generally post something of the form, "This is a commercial product, you're already paying for support, ask the company". I would be in favor of a similar strategy here. Thoughts?
Note: The question that inspired this is not a great example, since the product in question is a wrapper around standard open-source packages. Nonetheless the site will inevitably face other examples in the future.

Personally I don't think we should restrict asking questions related to commercial products if the questions/answers could be useful to the community. However, practically speaking providing good answers may often not be possible if the products are black boxes without open-source code etc.

I think it is OK to ask such questions, users of productX might be here and have a quick answer. Or the support team of the productX might be here, too. Better to have answers here public, rather than buried in productX members only forums.

Here is the Help Center guidance about supporting your product on this site.

Even though I'm a supporter of free software, I do not see a problem in answering those questions.

It is hard to define the boundaries. Proprietary software can be only a part of the pipeline (e.g. Affymetrix, Ofxord Nanopore), or can be a somewhat standard tool (e.g. PAUP, many pop.gen tools, etc).
Stackexchange doesn't have any policy against commercial software or libraries; see here.
I do not see a problem if a commercial company will answer questions write here. This will be helpful.

Having said this, it is also ok to point out to the person, that he or she can contact their support.

I would actually encourage bioinfo companies to use this SE as a Q&A platform. IMHO, this will benefit both the companies and the users, no matter whether they are using their products or not. Stackoverflow has sponsored tags and welcomes companies (to bring money :-). I don't know if SE has a similar feature.

If they actually came to the site to answer questions then I'd be all for it. Experience dictates that they won't, unfortunately.

@DevonR I would give it a try. The better tagging system here might change something. Some companies seem to be using SO often. In addition, we could encourage companies to reply here, which may help. Well, wishful thinking?

Better hopeless optimism than the opposite :)

MinION users have official support channels and a community forum, but I'd much rather that users asked questions about MinION data analysis in a public forum. ONT has done about 3 community forum backend changes in the last 4 years, and haven't been all that interested in preserving the past history on the new forums. When the question can only be answered properly by communication with the company, I encourage the asker to contact ONT support (e.g. see this question about basecalling in the field).


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General guidelines on creating tag synonyms and naming (personal opinions)
Recently, there have been a few threads on creating tag synonyms. I think most of these are not really synonyms. The following shows my thoughts about what are synonyms and what are not. I will also talk about meta-tags, as it is related and has been mentioned a few times.
To begin with, I need to point out that concepts are often organized into a certain hierarchy. For example, alignment => nucleotide-alignment => read-alignment. This is related to the discussion below. I would also encourage people to have a look at the tag synonym page at SO. I don't think they are all perfect, but they are very informative.
In the SO tag synonym page, there are real synonyms like "format" vs "formats", "swift-3" vs "swift3" or "amazon-rds" vs "aws-rds". In these examples, the two tags are interchangeable. The relationship is obvious most of time.
What is harder to tell is semi-synonym: "swift3" vs "swift3.1" or "bash" vs "bash-function". For such pairs, one of the tag is conceptually the parent of the other tag. We create such synonyms when the child tag is unnecessarily narrow. Judging "unnecessity" is subjective. We have to take the habit of the community into account when making the decision.
Back to our recent examples:

sam vs bam. I think they are different enough and are not synonyms. "sam" is also conceptually the parent of "cram", "cSRA", "biohdf" and other binary representations of sam. If most of us still prefer to merge them, I would take "sam" as the master tag.
mapping vs read-mapping. As most others said, they are not because many "mapping" related problems have nothing to do with "read-mapping". Similarly, "read-mapping" is only one type of "alignment". They are not synonyms.

Now meta-tags. I think we might be sometimes confusing a meta-tag with a general tag. For example, "alignment" is a general tag, but it still sufficiently narrows the question down to a specific field. In contrast, the examples on the meta-tag page (e.g. "beginner" and "best-practice") are applicable to almost any fields. Here are some recent discussions related to meta tags:

format vs file-format. I think the latter is a synonym of the former. In addition to files, I am not sure what other formats we talk about daily. I am also ok to separate them out if others can prove me wrong, but "format" is definitely not a meta tag. A lot of existing questions are unrelated to format.
alignment vs sequence-alignment. Again, I think the latter is a synonym of the former because in bioinformatics, alignment is almost always applied to sequences or data structures derived from sequences (e.g. profiles, secondary structures or graphs). Alignment has a lot of applications, but it is only a small field in bioinformatics. "alignment" is not a meta-tag, either.

The problem with alignment is that it is used very often both for aligning reads to a genome and for aligning sequences to each other. Yes, both are aligning sequences, but sequence-aligning suggests classic multiple sequence alignments to me while read-alignment makes more sense for NGS analyses. The two are related but very different and each can have very different questions. I think we need different tags for these two types of alignment.

As for format vs file-format it's just a question of clarity. file-format is unambiguous and easy to understand while format is less so. Why not go for the less ambiguous name?

Read-alignment is a type of sequence-alignment. In addition to "file formats", what are the other "formats" we are dealing with? If there are no other formats that are not file formats, the two tags are synonym; if there are others, both tags are necessary. Either way, I don't think we should drop "format".

Yes, read alignment is indeed a type of sequence alignment. However, the word "alignment" is not sufficient to let you know what you're aligning and the techniques/tools used for read or MSAs are completely different. It is very easy to be an expert in one and not the other (one of the main uses for tags is to help experts find questions to answer). So making the main tags explicit (read-alignment and sequence-alignment for example) instead of the vague (alignment) seems like a good idea.

Same for format. Nothing wrong with it, but file-formats is clearer. I think it makes sense to make format a synonym of file-formats and have the latter as the main tag. The more explicit the tags, the less the chance of their being misunderstood and misused.

In my opinion, the main purpose of tags is to describe content the way, people can follow certain tags.
If we follow this logic, alignment or mapping are not very useful.

alignment could refer to two very different areas. I would prefer to have two different tags sequence-alignment and read-alignment. There is no point in having alignment meta-tag, since it doesn't describe the content well enough.
The same story with mapping, while read-mapping describes the content, mapping doesn't say anything on its own.

In my opinion we should use narrow tags, which describe the problem well enough.

It is interesting that you see read-alignment and sequence-alignment are distinct topics. To me, reads are sequences and therefore read-alignment is sequence-alignment, i.e. sequence-alignment is the parent of read-alignment. BTW, the title of the first bowtie paper is: "... alignment of short DNA sequences".

I do not think it is bad to have very general tags (like alignment), that can help to attract attention of competent people to put proper tags on (protein-alignment). However, I agree with non-using mapping tag for its ambiguity (you can map RAD tags or restriction sites to genome, prodein IDs to transcript IDs, ... there are plenty things to map).

@user172818 conceptually you're correct, but in practice people face very different problems. For sequence-alignment, it will be more about MSAs or pairwise global alignments, for read-alignment, there will be focus on read-mapping tools, I think (although I'm less familiar with the second). In any case, meta-tags are discouraged AFAIU. So we should choose tags, so that people can follow what's interesting conveniently; for that I would prefer having two different tags.


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Can we add a [bedops] tag?
I was wondering how tags are added. I'm a new user to this SE site, so I don't have the reputation to add new tags. Can we please add a bedops tag to make it easier to find, ask, and answer questions about this toolkit?

would definitely have bedops as one of the tag owing to its usage and popularity. I would definitely support it.

Yes, when people start to ask questions about bedops.

This early in the beta, there's a lot of flexibility in creating new tags. Users, even new ones, are unrestricted in which tags they can use, so tags are being created pretty quickly right now. There's some effort going into tag quality control right now, which is documented in some of the other questions in the meta.
Questions about bedops usage are definitely on topic here, and the bedops tag is definitely appropriate. That said, there's no way to create the tag until someone actually asks a question about bedops and tags it accordingly.
You're certainly welcome to seed the topic here with a couple of questions. Be careful though, the StackExchange community is wary about any content that feels too much like advertising. But done tactfully, using Bioinformatics.SE as a support forum for bedops should be fine. See relevant discussion here.


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Make tags [read-mapping] and [alignment] synonyms
As far as I can tell, there is no noticeable difference between the tags read-mapping and alignment. Three of the fifteen questions under these two tags use both tags, and the rest seem too similar to warrant any separation.
EDIT: Clearly I had failed to notice the quite significant difference between these terms. However, the ambiguity of the alignment tag and the way in which it is being used should be fixed. Terdon's answer below gives a good resolution of this issue.

No! When I hear "alignment" I will immediately think of protein or nucleotide multiple sequence alignments. I mean what is done by tools like t_coffee, mafft, clustal etc. That's what the word always meant when I started working in bioinformatics and I am sure I am not alone. Not everyone works in NGS analyses, you know :)
I would instead argue that precisely because the term alignment is not specific and can apply to many things, we should instead make more focused tags. So, we should have:

read-alignment : This should be a synonym of read-mapping (relevant meta post) and should be used for questions about aligning NGS reads to a genome.
sequence-alignment : this should be used for questions about sequence alignment (including protein, DNA and RNA alignments).

The alignment is a classic meta tag since there is no way of knowing what type of alignment it is describing without an additional tag to clarify. it should therefore be removed and not used at all.

That's fine until someone wants to make salmon or kallisto-specific questions, since there the distinction between mapping and alignment is clear.

I’m not even sure I’d call Salmon etc. mapping tools; rather, they’re alignment-free quantification tools. But it’s certainly true that kmer-based identification (or similar methods) is mapping, yet not necessarily alignment.

I think these tags are two different things. Reads mapping refers to a process when sequencing to find the position of a read to a reference genome while alignment is comparing two (or more) sequences.
Both can be DNA, but one can align also proteins, but I haven't heard of read-mapping proteins. For instance one can align some orthologous or paralogus genes/proteins which don't need to be reads.
That said, the excerpts should make clear the distinction (if the community agrees with this) to facilitate the usage of the right tag.


text:
How do we feel about questions that are essentially about text parsing?
A lot of the daily tasks of a bioinformatician can be boiled down to simple text parsing. Yes, we will be dealing with text files containing some form of biological data, but the answer might not really require any biological knowledge at all. For example, this question was posted on Unix & Linux today:

I have 2 files. File1 is:
chr19 4124051 4124250 1
chrX  154458151   154458200   2
chr22 37019451    37019600    3
chr15 74995401    74995550    4
chr12 128823901   128824100   5

and File2 is:
chr19 4124051 4124250 1   CUP
chr15 74995401    74995550    4   CUP
chr12 128823901   128824100   5   CUP
chr12 122752651   122752950   8   CUP
chr13 113297001   113297350   9   CUP

and I would like to have a File3 like this:
chr19 4124051 4124250 1 CUP
chrX  154458151   154458200   2
chr22 37019451    37019600    3
chr15 74995401    74995550    4 CUP
chr12 128823901   128824100   5 CUP

I'd like to merge the two files according to column 4 of File1, and
  adding values of column 5 from File2 to the last column of File1
  whenever there is a match.

This is obviously someone working in bioinformatics but the question itself is not really about bioinformatics. Nevertheless, it is relatively typical of the type of thing a bioinformatician does every day.
So, should we allow such questions even if they could be answered by anyone with knowledge of regular expressions and basic text parsing tools? If the question is one that a bioinformatician could encounter, should we consider it on topic even if it can be expressed as a general text parsing issue?

I think as soon as we mention the tool we want to use, it should be off-topic and worth migrating? Otherwise we will just be duplicating content over SE network?

@zx8754 first, the OP often doesn't know the tool. More importantly, the issue with text parsing Qs is that they are very often specific to the particular data being parsed. So duplicates aren't that clear. Also, I know I spend a lot of my time doing this sort of thing and very often help colleagues with it. Text parsing is very relevant to bioinformatics. Finally, there are sometimes considerations that a layperson won't be aware of (I can think of FASTA parsing questions, for example, where the OP didn't explain that the sequence can span multiple lines). Those are better served here.

Yes, agreed, if OP doesn't mention the tool, then it will be OK, as it will collect all solutions using different tools. But once the tool is specified, then regardless of bio knowledge anyone with particular tool proficiency would be able to answer the question, hence duplication over SE network and needs migrating (and most likely dupe hammered). Besides, I think most of SE traffic is coming form Google searches, so why would it matter which SE the Q is posted.

@zx8754 actually, we never migrate away a question if it is on topic on the site where it was posted. If we decide these are also on topic here, they should not be migrated. The only case for migration would be if we decide they're explicitly off topic here.

I would say we should allow these, yes. I opened a similar discussion about questions pertaining to biology and the consensus there seems to be clearly in favor of allowing them.
I feel this site only makes sense if our scope is essentially "Any question that a bioinformatician might face in the process of doing their job". We should aim to be a one-stop site for all questions that could be affecting someone trying to do bioinformatics. And since so much of bioinformatics is essentially parsing text files, it makes sense to me to allow them here.
I have seen such questions all over the place in the Stack Exchange network over the years. They are posted on Stack Overflow, Unix & Linux, Ask Ubuntu, and probably other sites too. I think all of those should come here and find a home.
Naturally, this would only apply if the text parsing in question is somehow connected to bioinformatics and not something like extracting text from a movie subtitle file or whatever.

Agreed with the explicit caveat that the text being processed should have at least a vague relevance to bioinformatics/biology. We don't want questions related to using grep to find something specific in /etc :)

@DevonRyan yes, of course. I added a note to that effect.

I agree, plus, I think often it takes a someone with a clear understanding of the file format to provide a good answer. For example, this SO question made no reference to bioinformatics until I added some tags and it was only then that it got a good answer (from Konrad). Other answers clearly didn't understand that FASTA permits multiple sequence lines https://stackoverflow.com/questions/44264127/filtering-a-weird-text-file-in-python Sometimes it's even worse and the OP actually describes the file format wrongly, so it takes a bioinformatician to know this and provide the correct answer

@Chris_Rands yes, precisely. I have often had to clarify such things to people answering bioinformatics-related parsing questions on [linux.se] too.

On one hand, posting this kind of question in Unix & Linux SE or stackoverflow may cause general and/or very efficient solutions to show up, due to the presence in those communities of people quite capable with general text handling skills.
On the other hand, such people might not be aware of bioinformatics tools specifically designed to efficiently solve the problem. If such tools exist, contributors to bioinformatics SE are more likely to know about them, and the answer may be of interest to a higher proportion of the readers here than in stackoverflow or Unix & Linux SE.
It is of course up to the poster to decide whether to post here or in another site, and I think we should probably accept such questions if we think that my "On the other hand" point is relevant, that is, on the basis that someone may come up with an answer based on the use of a tool specifically used in the bioinformatics field.

Of course it is up to the poster! That's not debatable. The question is whether we will consider such topics on topic here or not. Any form of text parsing question is already on topic on sites like [so], [linux.se], [ubuntu.se] and even [apple.se], [su] and [elementaryos.se]. We're not going to move them if they're on topic where they were asked. But should we accept them if they are asked here?

I would say that we should generally accept them on the basis that they can be of interest to other bioinformaticians, and especially on the basis that someone may provide an answer based on specific tools for bioinformatics.

Yes, me too. Could you edit your answer to clarify that that is your position then please?

I tried to edit my post accordingly.

I think we should accept these questions, if they relate to biological data, for two reasons:

The answer might reasonably be of interest to other bioinformaticians (This is mentioned in other answers).
An acceptable solution might reasonably use a framework commonly used in bioinformatics, but not by anyone else. A hypothetical example: One could imagine that an acceptable answer converts the files to BED format and then merges them using bedtools.
On other SE sites I would consider using bedtools for anything as too specific/off-topic.


text:
Tag [file-formats] or [data-formats] to replace [formats] tag
As of now, 5 questions have been tagged with formats and since bioinformatics in practice is 80%+ file format conversion, we can expect many more such questions!
I jest about the 80% bit...kind of...
Either way, it's important to get this tag right early on to set the appropriate tone. Just formats strikes me as a bit vague, and my first thought was to replace it with file-formats. But one could argue that this topic is relevant for converting data between different formats, even if the data is never stored in an actual file (such as in streaming processing). So perhaps data-formats is a more accurate term?
I worry that the latter, while technically more accurate, might be a bit pedantic and a turn-off for newer members of the community.
UPDATE:
Ok, I re-tagged 6 posts. Edits pending approval.

You mean it's actually 90%, right? :P

My vote goes to file-formats. While you can argue, as you did, that data-formats would be more accurate, since most of us are working on *nix systems where, famously, everything is a file, I think we can wing it with file-formats.
After all, even a pipe is actually a file, really. More to the point, as you said, the distinction is rather technical and I think we should err on the side of not confusing novices as opposed to appeasing the pedants.
In any case, formats is a classic meta tag. Formats of what? Who formats and what are they formatting? No, file-formats seems far better and instantly understandable by novice and expert alike.

I was uncertain when I started writing the question, but I had all but made up my mind by the time I finished writing it. I agree, file-formats is the way to go. I'll leave this open for a bit longer to give time for dissenting or alternative comments, then I'll clean up the tags.

@DanielStandage by the way, thanks for all these tag posts! They're a pain to write but essential if we're going to have a useful tagging system. Much appreciated!

No, I don't think we should rename "format". To me, "format" is instantly the first tag I can think of when dealing with file formats. Users will use the "format" tag from time to time anyway. In fact, if you search "format" at SO, "format" and "formatting" are by far the mostly used tags.
In addition, if you think "format" is meta-ish, "file-format" is, too, just in a little narrower scope. You still don't know whether a question tagged with file-format is about a gene annotation format, an alignment format or a variant format.


text:
Replace sam and bam tags with a single sam-or-bam tag
The discussion in the recent suggestion to make sam and bam synonyms seems inconclusive with users falling on either side of the argument.
I propose we instead remove both tags and create sam-or-bam, or sam-and-bam, or something along those lines that would cover both. We can then make both sam and bam synonyms of sam-or-bam and thereby avoid the cognitive dissonance of having a question about sam be tagged as bam or vice versa while still having the benefit of a single tag for these obviously related subjects.
Thoughts?

Would a "sam-or-bam" tag automatically be proposed when a user types "sam" or "bam"?

@bli Yes. If the tag has been created, typing any part of it would show the sam-or-bam as an option.

I'd prefer making sam and bam synonyms over this. I wouldn't hold off on making those two synonyms just because one person (me) opposed it!

You're not alone. I also disagree as do at least three more people who upvoted your answer. As many as have upvoted the question suggesting the merge. Now, this compound tag might indeed not be the best solution either, I'm just throwing suggestions around to see what will stick, but it isn't in any way only because you disagree!  Making them synonyms just feels wrong to me; if a question is specific to a sam file, adding bam to it seems off.

Ah, I hadn't noticed the up votes! Truth be told, I really don't have any better suggestion than your proposal, other than perhaps just forgetting the synonyms altogether.