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

[João Fadista]

Hi Simon,

Thanks for the fast reply. It would be great if you could share your script.

Best regards,
João

 

-----Original Message-----
From: bioc-sig-sequencing-bounces at r-project.org [mailto:bioc-sig-sequencing-bounces at r-project.org] On Behalf Of simon andrews (BI)
Sent: Monday, May 11, 2009 10:51 AM
To: bioc-sig-sequencing at r-project.org
Subject: Re: [Bioc-sig-seq] calculate alignable portion of the genome

 

> -----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

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