I have the treatment groups. I have their bigwig files and I want to find the enrichment of each group based within specific regions contained a BED file.

I'm using deeptools:

computeMatrix reference-point -a 1000-b 1000 -R $peak -S $bigwig --skipZeros

The matrix I get is has minimal to no enrichment with 0.0ish values. Half of the values should be greater than 0.15. What may cause such result?

Steps:

1. Bam file with alignment over the whole genome.
2. Convert to bigwig (CPM normalization)
3. Use that to calculate coverage around the wanted regions.

Is there anything I'm not understanding correctly?

Thank you in advance.