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

[Martin Morgan]

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