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
