Extract co-ordinate for iCLIP data?

Question

[PK]

Hi All, I have to fetch the chromosome coordinate of genes from the transcription start site to the end of the each nearest iCLIP read. I tired with bedmap tool. but it is just simply giving the total length.

Thanks,

Answer 1

[Istvan Albert]

I am not sufficiently familiar with bedops to identify the correct tool in that suite.

But I believe that when using bedtools the closest operator might give you what you need.

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