Finding exact matches between query and subject gtf files

Question

[Sarah]

Hello,

I would like to compare 2 gtf files and find in 1st gtf only cds that include 2d gtf cds fully (all exons). I am currently using function findOverlaps (package GenomicRanges), but I didn't succeed achieving what I want.

I would appreciate any help

[iraun]

Hi! Not sure if I follow what is your goal, but bedtools intersect works for these kind of tasks.

Answer 1

[GenoMax]

Use a toolkit like agat that is designed for working with annotation files : https://agat.readthedocs.io/en/latest/tools/agat_sp_compare_two_annotations.html