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RnaQC tool help

RnaQC (2024_08-110-g317f43b9)

Calculates QC metrics for RNA samples.

Mandatory parameters:
  -bam <file>                Input BAM/CRAM file.

Optional parameters:
  -housekeeping_genes <file> BED file containing the exon region of housekeeping genes.
                             Default value: ''
  -roi <file>                BED file containing the target region of the analysis.
                             Default value: ''
  -out <file>                Output qcML file. If unset, writes to STDOUT.
                             Default value: ''
  -splicing <file>           TSV file containing spliced reads by gene.
                             Default value: ''
  -expression <file>         TSV file containing RNA expression.
                             Default value: ''
  -ref <file>                Reference genome FASTA file. If unset 'reference_genome' from the 'settings.ini' file is used.
                             Default value: ''
  -min_mapq <int>            Set minimal mapping quality (default:1)
                             Default value: '1'
  -txt                       Writes TXT format instead of qcML.
                             Default value: 'false'

Special parameters:
  --help                     Shows this help and exits.
  --version                  Prints version and exits.
  --changelog                Prints changeloge and exits.
  --tdx                      Writes a Tool Definition Xml file. The file name is the application name with the suffix '.tdx'.
  --settings [file]          Settings override file (no other settings files are used).

RnaQC changelog

RnaQC 2024_08-110-g317f43b9

2023-03-22 Added optional target region.
2022-07-12 Made housekeeping genes optional.
2022-05-12 Changed TPM cutoffs.
2022-04-27 Initial version.

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