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.
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.
