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agat_sp_fix_features_locations_duplicated.pl#

DESCRIPTION#

The script aims to modify/remove feature with duplicated locations. Even if it not an error by itself in a gtf/gff file, it becomes problematic when submitting the file to ENA (after convertion). To modify locations, AGAT modify the UTRs (when available) by shortening them by 1 bp (and consequently the Parent features and the exons accordingly)

  • Case1: When isoforms have identical exon structures, AGAT removes duplicates by keeping the one with longest CDS;
  • Case2: When l2 (e.g. mRNA) from different gene identifier have identical exon but no CDS at all, AGAT removes one duplicate);
  • Case3: When l2 (e.g. mRNA) from different gene identifier have identical exon and CDS structures, AGAT removes duplicates by keeping the one with longest CDS);
  • Case4: When l2 (e.g. mRNA) from different gene identifier have identical exon structures and different CDS structures, AGAT reshapes UTRs to modify mRNA and gene locations);
  • Case5: When l2 (e.g. mRNA) from different gene identifier overlap but have different exon structure. In that case AGAT modified the gene locations by clipping UTRs;

SYNOPSIS#

agat_sp_fix_features_locations_duplicated.pl --gff infile  [-o outfile]
agat_sp_fix_features_locations_duplicated.pl --help

OPTIONS#

  • -f, --file, --gff3 or --gff

    Input GTF/GFF file.

  • -m or --model

    To select cases you want to fix. By default all are used. To select specific cases write e.g. --model 1,4,5

    Case1: When isoforms have identical exon structures AGAT removes duplicates by keeping the one with longest CDS; Case2: When l2 (e.g. mRNA) from different gene identifier have identical exon but no CDS at all (AGAT removes one duplicate); Case3: When l2 (e.g. mRNA) from different gene identifier have identical exon and CDS structures (AGAT removes duplicates by keeping the one with longest CDS); Case4: When l2 (e.g. mRNA) from different gene identifier have identical exon structures and different CDS structures (AGAT reshapes UTRs to modify mRNA and gene locations); Case5: When l2 (e.g. mRNA) from different gene identifier overlap but have different exon structure. In that case AGAT modified the gene locations by clipping UTRs;

  • -v or verbose

    Add verbosity.

  • -o, --out, --output or --outfile

    Output file. If none given, will be display in standard output.

  • -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).

  • --help or -h

    Display this helpful text.