vlookup type array matching command for BED analysis

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7.8 years ago

rishi ▴ 10

Hi. I am a beginner in computational biology.

I have a bed file with four columns; CHR#, START, STOP, READVALUE. I have a second bed file with five columns; CHR#, START, STOP, ENSG-ID, GENE-ID. The CHR#s are not in order.

I want to create a third bed file which intersects the START and STOP intervals of File 1 and 2 (or 2 and 1) and prints the READVALUE as a sixth column after the GENE-ID column. I've tried my best but am unable to do so. What command(s) should I try?

Thanks in advance for the help.

ChIP-Seq unix • 1.8k views

ADD COMMENT • link 7.8 years ago by rishi ▴ 10

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I've tried my best but am unable to do so

what have you tried ?

ADD REPLY • link 7.8 years ago by Pierre Lindenbaum 161k

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I've tried intersecting in different ways but doesn't work. I need all the six columns. I guess I have to write something in awk but I don't know how to

ADD REPLY • link 7.8 years ago by rishi ▴ 10

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Have you looked at BedTools intersectBed (http://bedtools.readthedocs.io/en/latest/content/tools/intersect.html )?

ADD REPLY • link 7.8 years ago by GenoMax 141k

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Got the answer! Adding -wb and then editing made it possible. Thank you

ADD REPLY • link 7.8 years ago by rishi ▴ 10

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