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Old 10-28-2014, 06:42 PM   #19
Location: Auckland

Join Date: Sep 2011
Posts: 72

When you used the reference GTF, did you also set the option to only map to annotated genes (-T/--transcriptome-only)?
I'm a bit confused as to why you are expecting Tophat and Bowtie to behave identically. Tophat is splice-aware, bowtie is not. I don't understand why you would ever use Bowtie (or any other non-splice-aware mapper) to map RNA-derived sequence to a genome.
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