Thanks, Martin. I have been looking at it. Neel
On Dec 11, 2010, at 9:43 PM, Martin Morgan wrote: > 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 > 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
