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agat_convert_genscan2gff.pl#

DESCRIPTION#

The script takes a genscan file as input, and will translate it in gff format. The genscan format is described here: http://genome.crg.es/courses/Bioinformatics2003_genefinding/results/genscan.html /! vvv Known problem vvv /! You must have submited only DNA sequence, wihtout any header!! Indeed the tool expects only DNA sequences and does not crash/warn if an header is submited along the sequence. e.g If you have an header ">seq" s-e-q are seen as the 3 first nucleotides of the sequence. Then all prediction location are shifted accordingly. (checked only on the online version http://argonaute.mit.edu/GENSCAN.html. I don't know if there is the same pronlem elsewhere.) /! ^^^ Known problem ^^^^ /!

SYNOPSIS#

agat_convert_genscan2gff.pl --genscan infile.bed [ -o outfile ]
agat_convert_genscan2gff.pl -h

OPTIONS#

  • --genscan or -g

    Input bed file that will be convert.

  • --source

    The source informs about the tool used to produce the data and is stored in 2nd field of a gff file. Example: Stringtie,Maker,Augustus,etc. [default: data]

  • --primary_tag

    The primary_tag corresponf to the data type and is stored in 3rd field of a gff file. Example: gene,mRNA,CDS,etc. [default: gene]

  • --verbose

    add verbosity

  • -o , --output , --out , --outfile or --gff

    Output 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.