How to handle multiple overlap and choose closest one?
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10 weeks ago
barrypraveen ▴ 100

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?

RNA-Seq bedtools • 231 views
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