agat_sp_add_splice_sites.pl#
DESCRIPTION#
The script aims to add splice sites features (five_prime_cis_splice_site and three_prime_cis_splice_site) to gtf/gff file. The splice sites are deduced from CDS features.
SYNOPSIS#
agat_sp_add_splice_sites.pl --gff infile --out outFile
agat_sp_add_splice_sites.pl --help
OPTIONS#
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--gff, -f, --ref or -reffile
Input GTF/GFF file.
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--out, --output or -o
Output file (default GFF3 - see config to modify output format).
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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 yo the possibility to use your own AGAT config file (located elsewhere or named differently).
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--help or -h
Display this helpful text.