I recently installed Ubuntu 16.04 (because I was still using 12.04). But it seems my bedtools scripts don't work properly anymore. I can't figure out how to use the new bedtools for my old ways. What I want to do is get the number of reads from a bam file, per interval from a bed file. It was very simple with my old version of Ubuntu and bedtools:
bedtools coverage -abam file.bam -b All_peaks.bed > file.cov.txt
But this doesn't seem to work anymore. I used to get small files as results (~3MB), but now huge files are created (~4GB) including read names??
I am using bedtools v2.25 now.