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

[simon andrews (BI)]

I've put the script up at:

http://www.bioinformatics.bbsrc.ac.uk/downloads/make_all_mismatch_fragments.pl

I've put in a few comments to try to explain what it's doing, but it wasn't really written with public consumption in mind :)

Simon. 

> -----Original Message-----
> From: João Fadista [mailto:Joao.Fadista at agrsci.dk] 
> Sent: 11 May 2009 10:13
> To: simon andrews (BI); bioc-sig-sequencing at r-project.org
> Subject: RE: [Bioc-sig-seq] calculate alignable portion of the genome
> 
> 
> 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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