specified to use mm10_th2 index (to separate from using the noncompatible mm10 index generated by bowtie-build)
specified to use mm10_th2 index (to separate from using the noncompatible mm10 index generated by bowtie-build)

this index was created from within the mm10 directory with the commands:
rsync -avzP rsync://hgdownload.cse.ucsc.edu/goldenPath/mm10/bigZips/ .
twoBitToFa mm10.2bit mm10.fa
bowtie2-build mm10.fa mm10_th2

davebridges/biomolecule-scripts,davebridges/biomolecule-scripts,davebridges/biomolecule-scripts