Does bedtools intersect output overlaps with isoforms?
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16 months ago
kmkdesilva ▴ 90

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?

bedtools isoforms • 404 views
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You do not give any details on your input files (format). But in general bedtools returns all overlaps, yes.

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

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16 months ago

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

Kevin

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