Hi, On Sun, Dec 12, 2010 at 2:14 PM, Neel Aluru <[email protected]> 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 -- 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 _______________________________________________ Bioc-sig-sequencing mailing list [email protected] https://stat.ethz.ch/mailman/listinfo/bioc-sig-sequencing
