[BioC] SOLiD color space data

[Neel Aluru]

Thank you all for the suggestions. I really appreciate it.

Raffaele, I used BWA and it also indexes the genome in color space. Are you doing small RNA analysis with SOLiD seq? If so, what are the steps in your analysis pipeline? Which files format (SAM or BAM) are you uploading into R?

Thank you,

Neel




On Dec 12, 2010, at 12:48 PM, rcaloger wrote:

> 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
> 
> 
> 
> 
> -- 
> 
> ----------------------------------------
> Prof. Raffaele A. Calogero
> Bioinformatics and Genomics Unit
> MBC Centro di Biotecnologie Molecolari
> Via Nizza 52, Torino 10126
> tel.   ++39 0116706457
> Fax    ++39 0116706487
> Mobile ++39 3333827080
> email: raffaele.calogero at unito.it
>       raffaele[dot]calogero[at]gmail[dot]com
> www:   http://www.bioinformatica.unito.it
> 
> 

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