I am trying to use bedtools multicov to count the reads that map to introns. For this I have constructed a bed6 file containing the intronic regions.
The problem is that I want to keep only reads that completely map to intronic regions (no splice junctions/ no exonic reads).
For this I run bedtools in the following way:
bedtools multicov -bams file1.bam file2.bam file3.bam -bed introns.bed -D -s -f 1
The thing is that the -f 1 option (Minimum overlap required as a fraction of each A) doesn't seem to work properly, as it does not report any reads.