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?
- Bam file with alignment over the whole genome.
- Convert to bigwig (CPM normalization)
- Use that to calculate coverage around the wanted regions.
Is there anything I'm not understanding correctly?
Thank you in advance.