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

[Neel Aluru]

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