bigWigAverageOverBed in.bw in.bed out.tab
This tool is part of UCSC Genome Browser's utilities.
The output columns are:
name - name field from bed, which should be unique
size - size of bed (sum of exon sizes
covered - # bases within exons covered by bigWig
sum - sum of values over all bases covered
mean0 - average over bases with non-covered bases counting as zeroes
mean - average over just covered bases
-bedOut=out.bed - Make output bed that is echo of input bed but with mean column appended
-sampleAroundCenter=N - Take sample at region N bases wide centered around bed item, rather
than the usual sample in the bed item.
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