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

[Neel Aluru]

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. 

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