Hello! I hope somebody can provide some insight into TopHat and Bowtie2 behavior. I have a data set that I aligned to a reference using Bowtie2 and Tophat, both running default settings. When I used Bowtie, the alignment rates were >90% for all samples. With Tophat, however, the rates were all around 45-55%. Since Tophat uses Bowtie, I'm not sure why the resulting alignment rates are so much lower. My best guess is that when Tophat calls Bowtie, it uses different settings than the default settings for a user using Bowtie directly, but I haven't been able to figure this out from the respective manuals. Could anyone explain why this might be? I'm curious because there's apparently something about my reads that is very sensitive to differences in aligners used, and I want to know what it is.
I'm not sure what additional information is needed to answer this question but I'm ready to provide it. Thank you!
ETA: I'm using Tophat2 and Bowtie2, latest versions of both