[Bioc-sig-seq] calculate alignable portion of the genome

[simon andrews (BI)]

> -----Original Message-----
> From: bioc-sig-sequencing-bounces at r-project.org 
> [mailto:bioc-sig-sequencing-bounces at r-project.org] On Behalf 
> Of João Fadista
> Sent: 11 May 2009 09:36
> To: bioc-sig-sequencing at r-project.org
> Subject: [Bioc-sig-seq] calculate alignable portion of the genome
> 
> Hi,
> 
> I would like to know if there is any functions in 
> Bioconductor (or other) that could help me calculate the 
> alignable portion of a genome (not human), given a reference sequence.
> When I say alignable portion I mean that I want to know all 
> the positions of the genome that can be covered uniquely by 
> reads of 36 bp and up to 2 mismatches.

I recently did this for a whole human chromosome using a Perl wrapper around bowtie[1].  It could do a whole chromosome against a full genome in a few minutes, so anything smaller would be much quicker.

I'm happy to share the script I used, but you'd need to adapt it for your own needs.  My script was just collecting statistics, but it would be a trivial change to make it write out the uniquely mapping fragments.

Simon.

[1] http://bowtie-bio.sourceforge.net