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

Neel Aluru naluru at whoi.edu
Sun Dec 12 20:14:01 CET 2010

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? 

Thank you,


On Dec 12, 2010, at 10:57 AM, Steve Lianoglou wrote:

> Hi Neel,,
> On Sat, Dec 11, 2010 at 9:26 PM, Neel Aluru <naluru at whoi.edu> wrote:
>> Thanks, Martin. I also have read and heard about doing everything in color space. But, all the short read aligners convert the csfasta files to fastq before mapping to the genome.
> I don't actually think this is true. I've just had to deal with some
> SOLiD data, and bowtie does everything in colorspace (you can give it
> the csfasta and qual files separately -- look for their -Q flag). Note
> that you have to align to a special color space index.
> I'd also be very surprised if BWA doesn't handle color space reads,
> since (i) you can specify building a color space specific indiex (in
> the bwa index ... command); and (ii) their paper says they handle
> color space reads. I think the fastq file you would use as input to
> BWA would just have the sequences in color space.
> The SHRiMP aligner also does colorspace ...
> -- 
> 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

Neel Aluru
Postdoctoral Scholar
Biology Department
Woods Hole Oceanographic Institution
Woods Hole, MA 02543

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