to annotate BEDPE files

Question

[Bogdan]

Dear all,

a simple question if I may ask you please : given a BEDPE file (a short example is shown below), which tools would you recommend for computing the annotations for END1 and END2 (in order to annotate with the closest TSS, closest TTS, or other regulatory features, such as enhancers, silencers, etc ) ?

chr1    x1  x2  chr2    y1  y2
10  58550000    58560000    10  58810000    58820000
10  16950000    16960000    10  17720000    17730000
10  112070000   112080000   10  112140000   112150000

thanks a lot !

-- bogdan

[loughrae]

I’d use bedtools closest. What do you want to do with the paired segments?

[Bogdan]

thank you.

regarding the paired segments, we will just compute some summaries, like promoter-enhancer, enhancer-enhancer, promoter-promoter.

[Lhl]

is this what you are looking for? https://github.com/imgag/ngs-bits/blob/master/doc/tools/BedpeGeneAnnotation.md