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?
You do not give any details on your input files (format). But in general bedtools returns all overlaps, yes.
Sorry, my inputs are in bed file format. Thank you
You can control what is output - can you please check the options for bedtools intersect, specifically the -wa -wb -wao et cetera options.
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