Be aware of the order of bigWigAverageOverBed output!
If the input bed file is short, it's fine - same order of input bed file.
If the input bed file is large (not sure how large will trigger this), the programme will sort the input by chromosome (e.g. chr1, chr2, ...) first and then output in order of sorted chromosome. Be careful of this!
glad to hear it helps :)
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