Comments (1)
Hi Rob,
This error would happen if your target BED file, and therefore the target and antitarget .cnn files, had integer chromosome names with no "chr" prefix, but the reference genome FASTA file does have the "chr" prefix in the sequence names. If that's the case (just check if the BED file has "1" instead of "chr1"), you can fix this by adding "chr" to the beginning of each line in your BED file, then re-running the pipeline.
Best,
Eric
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