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#
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-g, --gff or -ref
Input GTF/GFF file.
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-f or --fasta
Input fasta file.
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--of
Output fixed fasta file. If no output file is specified, the output will be written to STDOUT.
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--og
Output fixed GFF file. If no output file is specified, the output will be written to STDOUT
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-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).
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-h or --help
Display this helpful text.