Question: Does bedtools intersect output overlaps with isoforms?
0
gravatar for kmkdesilva
4 weeks ago by
kmkdesilva90
United States
kmkdesilva90 wrote:

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?

isoforms bedtools • 123 views
ADD COMMENTlink modified 4 weeks ago by Kevin Blighe66k • written 4 weeks ago by kmkdesilva90
1

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

ADD REPLYlink written 4 weeks ago by ATpoint40k

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

ADD REPLYlink written 4 weeks ago by kmkdesilva90
1
gravatar for Kevin Blighe
4 weeks ago by
Kevin Blighe66k
Kevin Blighe66k wrote:

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

Kevin

ADD COMMENTlink written 4 weeks ago by Kevin Blighe66k
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