utr_refine

Command utr_refine predicts or refine UTRs.

usage

$ ingenannot -v 2 utr_refine genes.gff transcripts.gff genes.utr.gff

positional arguments:

Gff_genes	Gene Annotation file in GFF/GTF file format to add/correct UTRs
Gff_transcripts	Transcript Annotation file in GFF/GTF file format used to add/correct UTRs
Output	Output Annotation file in GFF file format

optional arguments:

-h, –help	show this help message and exit
–utr_mode {longest,shortest,rank,all}	In case of several transcripts match the ORFs to extend, select the mode to add UTR [longest, shortest, rank, all], default=longest
–erase	Previous annotated UTRs will be deleted, instead of to be elongated, and so possibly reduced, default=False
–onlynew	Add only new UTR on genes without UTR, keep previous if available, default=False