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: [email protected] raffaele[dot]calogero[at]gmail[dot]com www: http://www.bioinformatica.unito.it _______________________________________________ Bioc-sig-sequencing mailing list [email protected] https://stat.ethz.ch/mailman/listinfo/bioc-sig-sequencing
