Does bedtools intersect output overlaps with isoforms?

Question

[Kash]

Hi

I am using bedtools intersect option to identify which regions in my file are overlapping with exons. One thing I am curious about, is if a gene has 5 isoforms with an exon common to each, does bedtools return all 5 for the overlap, or just 1?

[ATpoint]

You do not give any details on your input files (format). But in general bedtools returns all overlaps, yes.

[Kash]

Sorry, my inputs are in bed file format. Thank you

Answer 1

[Kevin Blighe]

You can control what is output - can you please check the options for bedtools intersect, specifically the -wa -wb -wao et cetera options.

Kevin