 fix for paired end mode tophat and bowtie2
 fix for paired end mode tophat and bowtie2

kbase/KBaseRNASeq,kbaseIncubator/KBaseRNASeq,kbaseIncubator/KBaseRNASeq,kbase/KBaseRNASeq,kbase/KBaseRNASeq,kbase/KBaseRNASeq,kbaseIncubator/KBaseRNASeq