How to count reads in bam per bed interval with bedtools

Question

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.

Answer 1

The order of -a and -b switched at some point. You want:

bedtools coverage -a All_peaks.bed -b file.bam > file.cov.txt

For reference, this is the end of the help output in version 2.25:

Default Output:  
     After each entry in A, reports: 
       1) The number of features in B that overlapped the A interval.
       2) The number of bases in A that had non-zero coverage.
       3) The length of the entry in A.
       4) The fraction of bases in A that had non-zero coverage.

And this is the equivalent output from version 2.19:

Default Output:  
     After each entry in B, reports: 
       1) The number of features in A that overlapped the B interval.
       2) The number of bases in B that had non-zero coverage.
       3) The length of the entry in B.
       4) The fraction of bases in B that had non-zero coverage.

Update: The change in behavior happened in version 2.24:

We have changed the behavior of the coverage tool such that it is consistent with the other tools. Specifically, coverage is now computed for the intervals in the A file based on the overlaps with the B file, rather than vice versa.