LuscombeU_annotationpolish

Description

R package for annotation polishing. This package can perform the following on base gff3 files:

1. Add 5' UTR based on CAGE bed files (add_five_prime_utr())
2. Add 3' UTR based on canonical polyA site using information from BSgenome (add_three_prime_utr_wrapper())
3. Clean manual gff3 annotation written by hand (clean_manual_anno())
4. Add unique identifier column ID (add_unique_id())
5. Create a list of operons from gene lists and CAGE non-SL peaks (make_operons())
6. Fix liftoff gff files previously fixed wrongly by AGAT (fix_liftoff_oikobase())
7. Prioritize one transcript model over another (pick_transcripts())
8. Split chimeric transcripts based on CAGE and liftoff (split_transcripts())
9. Assign transcript_id and gene_id when there is only ID and Parent (assign_IDs_from_ParentandID())
10. Rename Name based on grouping of gene_id (rename_Name_based_on_gene_id())

Installation

devtools::install_github("oist/LuscombeU_annotationpolish")