bedtools intersect with match on name column

Question

[corend]

I have files a.bed and b.bed

a.bed

chr1 10 20 geneA
chr1 30 40 geneB

b.bed

chr1 5 15 geneA
chr1 10 25 geneB

if I intersectbed those files I will obtain:

chr1 10 15 geneA
chr1 10 20 geneA

But I would like the name column to match between files so that i will obtain:

chr1 10 15 geneA

If name column does not match, I don't want to output the intersection. I can't find any option in intersectbed to "force identical name", any suggestions?

Answer 1

[ATpoint]

I would do a two-step process:

## First use the -wa -wb options to report both the entire entry of -a and of -b in case of overlap,
## and then use awk to check if the genes are the same.
## If so, keep the row, if not discard:

bedtools intersect -a a.txt -b b.txt -wa -wb | awk 'OFS="\t" {if ($4 == $8) print}' > intermediate.txt

## Then use intersect again to get the actual overlap:
bedtools intersect -a <(cut -f1-4 intermediate.txt) -b <(cut -f 5-8 intermediate.txt)

[corend]

Sorry, it is not working, here is the problem:

In the second step, you don't intersect line by line, so the problem is still the same. Just try it and you will see.

[ATpoint]

Based on the data you provided it gives exactly the result you intended:

[corend]

My bad, my example was not a MWE, I will validate your answer. If you replace 10 25 by 10 35 here you will see the problem.

Answer 2

[corend]

I finaly found out how to do it:

As I want a Chromosome and name match, I just make a bedfile in the format chr+name start end name, and it works well.