> -----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
