I am trying to use the Chicago pipeline. I started on playing around with Schoenfelder's data sets. - The digest file was generated from HiCUP. - I downloaded the bait coordinates from the supplemental Table1 and reformatted it to 'chr start end feature'. The 'feature' column is the original 'name' column. - Then I used 'create_baitmap_rmap.pl' to generate .rmap and .baitmap. But it produced an error: "Could not find '1 310' in digest_fragments hash - the digest file and oligo probes file appear to be incompatible." I am not quite familiar with perl. It looks like the logic is to map the oligo probes to digested fragments. If it is the case, would 'bedtools' be a more direct way to generate .baitmap? Thanks.