[BioC] SOLiD color space data

[rcaloger]

Hi Neel,
I work both with Illumina and SOLiD data.
As aligner I use SHRIMP,
http://compbio.cs.toronto.edu/shrimp
It indexes the genome in color space.
After mapping you can easily upload in R the mapped data.
Cheers
Raffaele

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.

>Sincerely,
>Neel

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




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----------------------------------------
Prof. Raffaele A. Calogero
Bioinformatics and Genomics Unit
MBC Centro di Biotecnologie Molecolari
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email: raffaele.calogero at unito.it
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