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Old 03-19-2014, 04:16 AM   #17
David Eccles (gringer)
Location: Wellington, New Zealand

Join Date: May 2011
Posts: 838

Originally Posted by dalesan View Post
I used bowtie v 1.0.0 to map to a filtered transcriptome containing only the longest gene model isoform of each gene.... For the genome alignment, I used tophat v.2.0.10 and observed that 75-80% of the reads aligned.
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.
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