agat_sp_clipN_seqExtremities_and_fixCoordinates.pl

DESCRIPTION

The script aims to clip the N's extremities of the sequences. The annotation from the sequence clipped are modified accrodingly to stay consistent

SYNOPSIS

agat_sp_clipN_seqExtremities_and_fixCoordinates.pl -g infile.gff -f infile.fasta  [ -o outfile ]
agat_sp_clipN_seqExtremities_and_fixCoordinates.pl --help

OPTIONS

  • -g, --gff or -ref

    Input GTF/GFF file.

  • -f or --fasta

    Input fasta file.

  • --of

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

  • --og

    Output fixed 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.