Does bedtools intersect output overlaps with isoforms?
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?
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Kevin Blighe
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Kash
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Kash
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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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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