I was wondering if you could answer a technical question about computational methods. I have generated contact maps (.hic format), but I can’t seem to figure out a nice way to extract the contacts for a list of paired region sets. Example input in BEDPE format:
chr5 1500000 1505000 chr5 1520000 1525000
chr11 1701000 1706000 chr5 1730000 1735000
with the output being something like:
chr5 1500000 1505000 chr5 1520000 1525000 105
chr11 1701000 1706000 chr5 1730000 1735000 78
where the new final column is the number of valid contact pairs between the two regions.
Are there tools for doing this that I just don’t know about? The juicer tool “dump” only works one coordinate set at a time, for large regions typically, and gets a whole matrix.
Berkley Gryder, Ph.D.
CCR, NCI, NIH
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