On Thu, Apr 19, 2012 at 1:55 PM, Peter Cock <p.j.a.c...@googlemail.com> wrote: > Hi Brad & Lance, > > I've been using Brad's bam_to_bigwig tool in Galaxy but realized > today (with a new dataset using a splice-aware mapper) that it > doesn't seem to be ignoring CIGAR N operators where a read is > split over an intron. Looking over Brad's Python script which > calculates the coverage to write an intermediate wiggle file, this is > done with the samtools via pysam. It is not obvious to me if this > can be easily modified to ignore introns. Is this possible Brad?
Looking into this a bit more, perhaps 'samtools depth' might be useful (bam2depth.c), maybe we can use this code to update your python+pysam code? Peter ___________________________________________________________ Please keep all replies on the list by using "reply all" in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/