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

[Steve Lianoglou]

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