bedtools intersect + subtract not adding up to original file?

Question

[asperlea]

Hi,

I have a BED file of features in the genome, for which I am trying to see how many bases overlap exons and how many don't. I used bedtools intersect to get a BED file that gives me the intersection of my features with an exon annotation from gencode, and bedtools sutract to get a BED file for the bases in my features that are not in exons. I then used awk -F'\t' 'BEGIN{SUM=0}{ SUM+=$3-$2 }END{print SUM}' to get the number of bases covered by each of these files but I am running into the strange issue that the bases of the intersection + the length of the subtraction do not add up to the number of bases in the original file. They add up to slightly more than the original.

Am I making some basic logic error, misunderstanding the intersect and subtract functionality or is something very strange going on?

Thanks,

Adriana

[asperlea]

Figured it out. The exons sometimes overlap resulting in the intersection being reported twice. Had to merge the exon annotation and everything worked.