I am trying to use bedtools to find intersections between H3K4me1 peaks and my regions of interest. Though I can see overlap on IGV, intersect returns 0 without any error messages.
Here is command I'm using and screenshot from IGV:
bedtools intersect -a gene.ROI -b wgEncodeBroadHistoneHuvecH3k4me1StdPk.broadPeak -u | wc -l
IGV screenshot: https://imgur.com/a/JYUzp
Is there something I'm missing?
Thank you, Kerry