agat_sp_kraken_assess_lift_coverage.pl

DESCRIPTION

The script takes as input gtf produced by Kraken (lift-over tool). It will analyse the kraken_mapped attributes to calculate the mapped percentage of each mRNA. According to a threshold (0 by default), gene with a mapping percentage over that value will be reported. A plot nammed geneMapped_plot.pdf is performed to visualize the result. /!\ The script handles chimeric files (i.e containg gene part mapped on the template genome and others on the de-novo one) /!\/!\ If the file is complete (containing kraken_mapped="TRUE" and kraken_mapped="FALSE" attributes), the script calcul the real percentage lentgh that has been mapped. Else the calcul is only based on feature with kraken_mapped="TRUE" attributes. So in this case the result most of time will be 100%. /!\/!\/!\ We met rare cases where Kraken mapped a feature to several locations of the de-novo genome. As result we could end up with mapping over > 100%. We report them as 100% mapped in the plot and a warning is raised to allow to check thoses cases.

SYNOPSIS

agat_sp_kraken_assess_lift_coverage --gtf infile.gtf [ -o outfile ]
agat_sp_kraken_assess_lift_coverage --help

OPTIONS

• -gtf

  Input gtf file produced by Kraken.

• --threshold or -t

  Gene mapping percentage over which a gene must be reported. By default the value is 0.

• --verbose or -v

  Verbose information.

• -o , --output , --out or --outfile

  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.