Hi all,
I had a question about running bowtie and tophat. If I run bowtie (flags: -p 4 -S --un -v 3; paired-end) independently of tophat, I get very different results when looking at what % of the reads were mapped to my reference genome (hg18). Bowtie by itself aligns 38,474,274 of 87,783,858 reads to hg18, whereas when tophat is run (flags: -p 4 -r 20; paired-end) it maps 69,190,587 reads. Does anyone have an idea why they would differ so greatly?
The data is 76bp paired end from cancer patients done on the GAIIx.
I had a question about running bowtie and tophat. If I run bowtie (flags: -p 4 -S --un -v 3; paired-end) independently of tophat, I get very different results when looking at what % of the reads were mapped to my reference genome (hg18). Bowtie by itself aligns 38,474,274 of 87,783,858 reads to hg18, whereas when tophat is run (flags: -p 4 -r 20; paired-end) it maps 69,190,587 reads. Does anyone have an idea why they would differ so greatly?
The data is 76bp paired end from cancer patients done on the GAIIx.
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