RNASeq Preprocess Arguments | COMO Documentation

The arguments used in the `/main/src/rnaseq_preprocess.py` file

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The default command for this block is as follows:

cmd = ' '.join(['python3', 'rnaseq_preprocess.py',
                '--context-names', '"{}"'.format(context_names),
                '--gene-format', '"{}"'.format(gene_format),
                '--taxon-id', '"{}"'.format(taxon_id),
                '--{}'.format(preprocess_mode)])

Argument	Required?	Description
`--context-names`	Yes	A list of cell types
`--gene-format`	Yes	The format your gene input is in
`--taxon-id`	Yes	The BioDBNet Taxon ID
`--create-matrix OR --provide-matrix`	Yes	Should the gene matrix be created, or are you providing a matrix?