19 Apr
2012
19 Apr
'12
8:26 a.m.
On Thu, Apr 19, 2012 at 1:55 PM, Peter Cock <p.j.a.cock@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