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

Martin Morgan mtmorgan at fhcrc.org
Sun Dec 12 03:14:55 CET 2010

On 12/11/2010 06:12 PM, Neel Aluru wrote:
> Dear Bioc Users,
> I just have quick question about the SOLiD sequencing analysis. Does
> Bioconductor has any packages that can handle SOLiD color space data.
> I want to do some preliminary analysis such as converting them to
> fastq sanger format and fasta format of unique reads. Right now I am
> using some perl scripts that come with aligners (BWA/bowtie). I went
> through BioC mailing lists and some associated papers and they have
> mentioned that in future they will extend their usage to SOLiD. If
> you know about them, could you please share it!
> Thank you very much in advance.

Hi Neel -- I don't think there are any Bioc packages handling color
space; it would seem like one would want to carry color space through
alignment / variant calling / ..., rather than converting to fastq? Martin

> Sincerely, Neel
> Neel Aluru Postdoctoral Scholar Biology Department Woods Hole
> Oceanographic Institution Woods Hole, MA 02543 USA 508-289-3607
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