Hello everyone,

In my gff/gtf files, I have complete product names (proteins) for the up/down-regulated genes, and my edfeR-generated csv file contains only the gene_IDs and their statistics. After checking both gff/gtf files, I found that they only contain complete product names but not gene names. Therefore, I have the following questions:

Can anyone suggest a Linux or R script that can extract the product names, and protein IDs from the gff.file corresponding to the gene_IDs present in the csv.file?

Is there any website where I can upload the whole list of gene products and find their linked genes?

I have tried using the UNIprot website, it showed me several gene names for the same product. Which one should I choose if all of them belong to the same organism I am dealing with?

Any guidance would be greatly appreciated.