[BioC] [Bioc-sig-seq] SOLiD color space data

Steve Lianoglou mailinglist.honeypot at gmail.com
Mon Dec 13 03:52:26 CET 2010


On Sun, Dec 12, 2010 at 2:14 PM, Neel Aluru <naluru at whoi.edu> wrote:
> Hi Steve,
> Thanks for your comments. Yes, I used BWA and it works in color space as well. As a first step, I trimmed the adaptors using cutadapt and wrote the output to BWA fastq (I believe that is csfastq). Then I indexed the genome in color space and mapped the reads. My mapping didn't work and that made me think if my files are in wrong format.
> Do you do small RNA analysis?

I don't at the moment, sorry.

I haven't stumbled on cutadapt before, thanks for pointing it out.
Unfortunately I'm not sure how to help you smoke out your problem. Are
you sure you have the correct adapter sequence you are trimming out?

If you expect your reads to be of a minimum length, maybe you can just
include the first X basepairs of the reads and try to align it that
way? (maybe there's something wrong with the 3' trimming)

Steve Lianoglou
Graduate Student: Computational Systems Biology
 | Memorial Sloan-Kettering Cancer Center
 | Weill Medical College of Cornell University
Contact Info: http://cbio.mskcc.org/~lianos/contact

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