On 12/11/2010 06:26 PM, Neel Aluru 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.
Hi Neel -- I'm not a color space wiz but see http://solidsoftwaretools.com/gf/ http://solid.community.appliedbiosystems.com/index.jspa Martin > Neel > > On Dec 11, 2010, at 9:14 PM, Martin Morgan wrote: > >> 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 >>> >>> _______________________________________________ Bioc-sig-sequencing >>> mailing list [email protected] >>> https://stat.ethz.ch/mailman/listinfo/bioc-sig-sequencing >> >> >> -- >> Computational Biology >> Fred Hutchinson Cancer Research Center >> 1100 Fairview Ave. N. PO Box 19024 Seattle, WA 98109 >> >> Location: M1-B861 >> Telephone: 206 667-2793 >> > > Neel Aluru > Postdoctoral Scholar > Biology Department > Woods Hole Oceanographic Institution > Woods Hole, MA 02543 > USA > 508-289-3607 > > > -- Computational Biology Fred Hutchinson Cancer Research Center 1100 Fairview Ave. N. PO Box 19024 Seattle, WA 98109 Location: M1-B861 Telephone: 206 667-2793 _______________________________________________ Bioc-sig-sequencing mailing list [email protected] https://stat.ethz.ch/mailman/listinfo/bioc-sig-sequencing
