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:[email protected]] > Sent: 11 May 2009 10:13 > To: simon andrews (BI); [email protected] > 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: [email protected] > [mailto:[email protected]] On Behalf > Of simon andrews (BI) > Sent: Monday, May 11, 2009 10:51 AM > To: [email protected] > Subject: Re: [Bioc-sig-seq] calculate alignable portion of the genome > > > > > -----Original Message----- > > From: [email protected] > > [mailto:[email protected]] On > Behalf Of João > > Fadista > > Sent: 11 May 2009 09:36 > > To: [email protected] > > 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 > > _______________________________________________ > Bioc-sig-sequencing mailing list > [email protected] > https://stat.ethz.ch/mailman/listinfo/bioc-sig-sequencing > _______________________________________________ Bioc-sig-sequencing mailing list [email protected] https://stat.ethz.ch/mailman/listinfo/bioc-sig-sequencing
