What is a good cutoff of mappability score from bigWigAverageOverBed ?
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4.5 years ago
Apoorva ▴ 280

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. What might be an appropriate cut-off for the scores from bigWigAverageOverBed ? The scores range from -7030 till 71800.

Also, I want to keep all negative values. So I cannot perform a log transformation. Is there any other way to scale or normalize the data so that I wont lose relevant information ?

ChIP-Seq bigWigAverageOverBed • 1.2k views

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