create_baitmap_rmap.pl: error:Could not find '1 310' in digest_fragments hash - the digest file and oligo probes file appear to be incompatible.

[Former user]

Hi,

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.

[MZ]

I have the same issue!

[Koi]

In case anyone is still having this issue, this is what worked for me:

The perl script is removing “chr” from the oligo file, but not from the digest file. So, if you’re working with hg38 and have “chr” in both files, only the regions from the oligo file will have the “chr” removed, and they won’t match with the regions from the digest file. My solution was to remove the “chr” from the digest file myself like this:

# First extract the header
head -2 Digest_Human_GRCh38_HindIII_None_08-13-56_29-09-2021.txt > Digest_Human_GRCh38_nochr_HindIII_None_08-13-56_29-09-2021.txt
# Now remove the first 3 characters from every line
tail -n +3 Digest_Human_GRCh38_HindIII_None_08-13-56_29-09-2021.txt | cut -c 4- >> Digest_Human_GRCh38_nochr_HindIII_None_08-13-56_29-09-2021.txt

And then use that as the digest file.

Cheers!