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
•
written
by
ioannis •
1 answer
You could just write a script in your favourite language to do this or look at bedtools' closest and intersect.
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