Gencode UTR fix

Gencode GTF does not differentiate UTR as 5' and 3' UTR but annotates all of them as UTR unlike Ensembl GTF which annotates UTR as five_prime_utr and three_prime_utr. Thus, gencode annotation creates difficulty while studying UTR type-specific processes such as alternative polyadenylation.

This package fixes UTR features in the third columns of Gencode GTF by converting UTR annotation into five_prime_utr and three_prime_utr similar to Ensembl. Package compares the location of UTR with CDS in GTF and annotates UTRs as five_prime_utr if UTR is located before CDS and three_prime_utr if UTR is located after CDS.

Setup

pip install cython
pip install -e git+https://github.com/MuhammedHasan/gencode_utr_fix.git#egg=gencode_utr_fix

Run

gencode_utr_fix --input_gtf gencode.v29.annotation.gtf --output_gtf gencode.v29.annotation_utr.gtf

Test

pytest tests/

Cite

This package is based on pyranges and designed for lapa so cite the PyRanges and LAPA if you are using this package for research:

PyRanges: http://dx.doi.org/10.1093/bioinformatics/btz615

LAPA: https://www.biorxiv.org/content/10.1101/2022.11.08.515683v1