Reduce GTF

Each organism processed by DEGenome will need a reduced GTF, i.e. a “gen_pos.tsv” file.

The gtf_to_gen_pos.py CLI module converts a GTF genome annotation file from GENCODE, Ensembl, or NCBI into a smaller, simpler, and more metadata-rich TSV gene position (“gen_pos”) file. The purpose is to speed up, simplify, and enrich downstream pipelines that require only data on genes, and not e.g. transcripts or exons.

Example GTF files

• Human (Homo sapiens), from GENCODE

• Mouse (Mus musculus), from GENCODE

• Thale cress (Arabidopsis thaliana), from Ensembl

• Worm (Caenorhabditis elegans), from Ensembl

• Rat (Rattus norvegicus), from Ensembl