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Old 03-19-2014, 04:40 AM   #18
Location: portugal

Join Date: Feb 2011
Posts: 15

Originally Posted by gringer View Post
Is there any particular reason why you used bowtie and not bowtie2? Were you specifically telling tophat to use bowtie, rather than bowtie2 (the default)?

I ask because if the bowtie versions are different, you'll be comparing a bit more than just genome vs transcriptome.

Additional question, did you use the transcriptome GTF file when mapping using tophat? I assume not, because that is likely to result in all transcriptome reads being picked up.
Actually, there was no particular reason that I chose to use bowtie 1. I just read up on the differences between bowtie 1 and 2 now, and it seems like bowtie2 has some nice improvements (affine gaps, local alignments, better ways to handle read pairs). Looks like I'll be re-running my pipeline one more time to see what the differences are in one alignment method vs another.

And yes, I did tell tophat to use bowtie 1. I did in fact use the transcriptome GTF file when mapping with tophat. I don't think it would pick up all transcripts because my transcriptome index file was indexed using a fasta file of only the longest/most representative gene models for each gene.

In your experience, have you noticed a big difference between bowtie 1 and 2? Does it warrant that I re-do my analysis?

Thanks for your questions!
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