I am mapping 50 bp SOLiD RNA-Seq reads to the mouse genome.
When I use bowtie, I get ~60% mapping (I am running bowtie with -e 950 as has been suggested elsewhere for mapping SOLiD runs with bowtie)
As there was no direct way to give tophat the -e option, I changed line 872 in the tophat python script from
to
When I run tophat with this option, I still get very poor mapping, of about 25%
Why is there this discrepancy, as one would assume that all of the unspliced mapping that bowtie does should be reproducible by tophat ?
Vineeth
When I use bowtie, I get ~60% mapping (I am running bowtie with -e 950 as has been suggested elsewhere for mapping SOLiD runs with bowtie)
As there was no direct way to give tophat the -e option, I changed line 872 in the tophat python script from
Code:
bowtie_header_cmd = [bowtie_path, "--sam"]
Code:
bowtie_header_cmd = [bowtie_path, "--sam", "-e 950"]
Why is there this discrepancy, as one would assume that all of the unspliced mapping that bowtie does should be reproducible by tophat ?
Vineeth
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