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agat_sp_filter_by_mrnaBlastValue.pl#

DESCRIPTION#

The script aims to remove from a gff file all the sequence that have a similarity over THRESHOLD with another sequence (will keep only one). This is typically useful when creating a list of mRNA to use to train abinitio gene finder. A reciprocal blast of the sequences need to have been performed prior to the use of this script in order to get the blastp input file.

SYNOPSIS#

agat_sp_filter_by_mrnaBlastValue.pl --gff infile.gff --blast blastfile --outfile outFile
agat_sp_filter_by_mrnaBlastValue.pl --help

OPTIONS#

  • --gff

    Input GTF/GFF file.

  • --blast

    The list of the all-vs-all blast file (outfmt 6, blastp)

  • --outfile

    The name of the output file. By default the output is the 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.