How to handle multiple overlap and choose closest one?

Question

[PK]

I have gtf file and i have disjointed exon file from DExSeq. I have to identify which exon is affected. for example my (i converted gtf to bed).

1 1400158 1400608 + ENSE000045454
1 1400158 1400544 + ENSE000045482

And i have my flattened exon bed file like this.

1   1400473 1400544 +

Since my exon can overlap with both coordinates of gtf , but i want to extract 1 1400158 1400544 + ENSE000045482 this one . How can i do this?

Answer 1

[Pierre Lindenbaum]

bedtools closest https://bedtools.readthedocs.io/en/latest/content/tools/closest.html