View Single Post
Old 12-12-2011, 01:59 AM   #1
swebb
Junior Member
 
Location: Edinburgh

Join Date: Jun 2009
Posts: 7
Default Coverage plots for paired end data

We have been creating coverage plots from chip-seq bam files using tools such as genomeCoverageBed or bamToBigWig. With single end chip-seq data we have not been extending read length to an inferred fragment size. However with paired end data it seems to make sense to do this if you have good quality pairs.

Are there any coverage plotting tools that will do this automatically? I.e look at aligned pairs and output coverage including the region between each.
swebb is offline   Reply With Quote