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 Bioc-sig-sequencing at r-project.org >>>> 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

Hi Steve, Thanks for your comments. Yes, I used BWA and it works in color space as well. As a first step, I trimmed the adaptors using cutadapt and wrote the output to BWA fastq (I believe that is csfastq). Then I indexed the genome in color space and mapped the reads. My mapping didn't work and that made me think if my files are in wrong format. Do you do small RNA analysis? Thank you, Neel On Dec 12, 2010, at 10:57 AM, Steve Lianoglou wrote: > 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 > Neel Aluru Postdoctoral Scholar Biology Department Woods Hole Oceanographic Institution Woods Hole, MA 02543 USA 508-289-3607