I have called (broad) peaks with macs2
macs2 callpeak -t A1.bam -c WT1.bam -g mm --broad
One of the found peaks appears to have a fold change of about 10
chr start end length pileup -LOG10(pv) fold_enrichment -LOG10(qv) 14 19415551 19419692 4142 37.35 29.87076 9.84997 24.22493
However, when I load this location in the IGV, both the control and the treatment look more or less the same.
In broad peak calling, the fold as calculated as the mean across the whole peak region, so it's a bit hard to see - but nevertheless it doesn't look like a fold of ~10 .
(Since macs2 omits duplicates, before loading IGV, I have marked duplicates with picard markduplicates, and filtered duplicates in IGV - so that is not the issue. When using markduplicates, non-primary alignments were not taken into account - just as in macs2 )
Would be glad for ideas what could the issue be.