What is a good cutoff of mappability score from bigWigAverageOverBed ?
0
0
Entering edit mode
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
ADD COMMENT

Login before adding your answer.

Traffic: 2201 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6