bigWig to bed for regions above/below threshold I'd like to threshold a bigWig file on a value and get all regions above or below that value in bed format. Ideally without too many file conversions. Are there any tools to do that?
You can do that with a bit of python:

#!/usr/bin/env python
import pyBigWig
threshold = 10  # Change me
bw = pyBigWig.open("file.bw")  # Change me
of = open("regions.bed", "w")  # Change me

for chrom, len in bw.chroms().items():
    intervals = bw.intervals(chrom)
    for interval in interals:
        if abs(interval[2]) &gt; threshold:
            of.write("{}\t{}\t{}\n".format(chrom, interval[0], interval[1]))
bw.close()
of.close()


You'll need to install pyBigWig (it's available via pip or conda install) and change the lines with Change me in them.