Very high negative scores from bigWigAverageOverBed
I have a bed file with genes I am interested in and Bigwig files from my ChIP-Seq experiment after subtracting input from treatment files using deeptools bamcompare. I used the bigWigAverageOverBed utility from UCSC to calculate the coverage. I only want to keep those that have a good mappability. The scores range from -260000 to +7000. I understand a higher negative value means more input levels but I am not sure why the values are as low as -260,000. What does that mean ?
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