Finding exact matches between query and subject gtf files

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

comparison gtf

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updated 3.8 years ago by GenoMax

• written 3.8 years ago by Sarah •

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

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written 3.8 years ago by iraun

1 answer

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

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written 3.8 years ago by GenoMax

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