agat_fix_small_exon_from_extremities.pl#

DESCRIPTION#

The script aims to extend the small exons to make them longer. When submitting annotation to ENA they expect exon size of 15 nt minimum. Currently we extend only the exon from extremities, otherwise we risk to break the predicted ORF. /! When we extend an exon and the CDS has to be extended too (because is was a partial CDS), we exit;

SYNOPSIS#

agat_fix_small_exon_from_extremities.pl -gff infile.gff --fasta genome.fa [ -o outfile ]
agat_fix_small_exon_from_extremities.pl --help

OPTIONS#

• -gff

  Input GTF/GFF file.

• -fa or --fasta

  Genome fasta file The name of the fasta file containing the genome to work with.

• --ct or --table or --codon

  This option allows specifying the codon table to use - It expects an integer (1 by default = standard)

• --size or -s

  Minimum exon size accepted in nucleotide. All exon below this size will be extended to this size. Default value = 15.

• -o , --output , --out or --outfile

  Output GFF file. If no output file is specified, the output will be written to STDOUT.

• -v

  Verbose option, make it easier to follow what is going on for debugging purpose.

• -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.