PeakSeq Mappability Map says no mappable sequences?
I am trying to use PeakSeq to create a mappability map of the Drosophila melanogaster release 6 assembly based on 50-mer and 36mers. I can successfully create mappability files using compile.py but when I access the data every nucleotide has a mappability score of either 48 or 49 (no uniquely mappable sequences). This happens even if I make mappability maps for 1000-mer. Does anyone have advice on what to try?
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