Mapping chromosome locations to gene IDs

Question

[ioannis]

Hello community,

I have a data set (.txt format) that consists of chromosomes and locations like this for example:

NC_031974.1- 35234789

NC_031974.1 - 32458

NC_031972.1 - 458920

...

...

...etc

All these unique regions are significantly differentiated between my sample groups. My final goal is to find out what/where are these locations (which genes? are exons/introns/promoters? etc).

I am working on the latest release of a genome (Oreochromis niloticus). I have a .gff3 file with the gene annotation from NCBI (https://www.ncbi.nlm.nih.gov/genome/197?genome_assembly_id=293496) but UCSC and Ensembl do not have this assembly.

Does anybody know how to assign/map my locations using this .gff3 file? Any software or package that can do this connection between "locations" and "gene information"?

I appreciate any help!

Cheers,

Ioannis

Answer 1

[Jean-Karim Heriche]

You could just write a script in your favourite language to do this or look at bedtools' closest and intersect.

[ioannis]

Thanks for the advice. I will have a look at bedtools manual.