RNASeq Gen Arguments | COMO Documentation

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

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This file creates RNA sequencing matrices for total and mRNA preparation methods. As a result,this section is called twice, once with --prep-method set to "total", and the second time set to "mrna".

The default command for this block is as follows:

cmd = ' '.join(['python3', 'rnaseq_gen.py', 
      '--config-file', '"{}"'.format(trnaseq_config_file), 
      '--replicate-ratio', '"{}"'.format(rep_ratio),   
      '--batch-ratio', '"{}"'.format(group_ratio),        
      '--high-replicate-ratio', '"{}"'.format(rep_ratio_h),    
      '--high-batch-ratio', '"{}"'.format(group_ratio_h),   
      '--filt-technique', '"{}"'.format(technique),  
      '--min-zfpkm', '"{}"'.format(min_zfpkm),
      '--library-prep', '"{}"'.format(prep_method)])       

Argument	Required?	Description
`--config-file`	Yes	The configuration file name to use
`--replicate-ratio`	Yes	The proportion of replicates with expression required for high-confidence
`--batch-ratio`	Yes	The proportion of samples with expression required for gene
`--high-replicate-ratio`	Yes	The proportion of replicates with expression required for high-confidence
`--high-batch-ratio`	Yes	The proportion of replicates with expression required for high-confidence
`--filt-technique`	Yes	The filtering technique; one of: (1) `"quantile"`, (2) `"cpm"`, or (3) `"zfpkm"`
`--min-zfpkm`	Yes	The cutoff for CPM filtering, if using zFPKM as the `--filt-technique`
`--library-prep`	Yes	The library prepartion method; one of: (1) `"total"`, (2) `"mRNA"`, or `"SC"`