The script looks for other ORF in UTRs (UTR3 and UTR5) of each gene model described in the gff file. Several ouput files will be written if you specify an output. One will contain the gene not modified (intact), one the gene models fixed.
agat_sp_fix_fusion.pl --gff infile.gff --fasta genome.fa [ -o outfile ] agat_sp_fix_fusion.pl --help
Input GTF/GFF file.
-fa or --fasta
Input fasta file.
--ct, --codon or --table
Codon table to use. [default 1]
-t or --threshold
This is the minimum length of new protein predicted that will be taken in account. By default this value is 100 AA.
-s or --stranded
By default we predict protein in UTR3 and UTR5 and in both direction. The fusion assumed can be between gene in same direction and in opposite direction. If RNAseq data used during the annotation was stranded, only fusion of close genes oriented in same direction are expected. In that case this option should be activated. When activated, we will try to predict protein in UTR3 and UTR5 only in the same orientation than the gene investigated.
-v or --verbose
Output verbose information.
-o , --output , --out or --outfile
Output GFF file. If no output file is specified, the output will be written to STDOUT.
-c or --config
String - Input agat config file. By default AGAT takes as input agat_config.yaml file from the working directory if any, otherwise it takes the orignal agat_config.yaml shipped with AGAT. To get the agat_config.yaml locally type: "agat config --expose". The --config option gives you the possibility to use your own AGAT config file (located elsewhere or named differently).
-h or --help
Display this helpful text.