Hi Neel,, On Sat, Dec 11, 2010 at 9:26 PM, Neel Aluru <[email protected]> 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 _______________________________________________ Bioc-sig-sequencing mailing list [email protected] https://stat.ethz.ch/mailman/listinfo/bioc-sig-sequencing
