Hello Shaun, Would this tool generate the type of statistics you are interested in? NGS: Picard (beta) -> Insertion size metrics for PAIRED data Another option is to convert the BAM alignments to SAM and then interval format, then use "Operate on Genomic Intervals -> Cluster", followed by "Base Coverage of all intervals ", but this would be grouping the data, not providing statistics per paired read set. Hopefully one of these will work out for you or another useful idea will be suggested, Best, Jen Galaxy team On 2/1/12 5:33 AM, SHAUN WEBB wrote:

Hi all.

I am analysing paired end chip-seq samples. With single end reads I have seen people extend reads by an inferred insert size and then create coverage files in wig format.

I was wondering if there are any tools available for paired end data that will create a coverage file by looking at properly mapped paired ends in a bam file and extending coverage across the distance between them.

Thanks Shaun Webb

-- Jennifer Jackson http://usegalaxy.org http://galaxyproject.org/wiki/Support