CNVKIT_IMPORT-RNA(1) User Commands CNVKIT_IMPORT-RNA(1)

cnvkit_import-rna - Convert a cohort of per-gene log2 ratios to CNVkit .cnr format.

usage: cnvkit.py import-rna [-h] [-f NAME] -g FILE [-c FILE]

[--max-log2 FLOAT] [-n NORMAL [NORMAL ...]]
[-d PATH] [-o FILE] [--no-gc] [--no-txlen] FILES [FILES ...]

Tabular files with Ensembl gene ID and number of reads mapped to each gene, from RSEM or another transcript quantifier.

show this help message and exit
Input format name: 'rsem' for RSEM gene-level read counts (*_rsem.genes.results), or 'counts' for generic 2-column gene IDs and their read counts (e.g. TCGA level 2 RNA expression).
Location of gene info table from Ensembl BioMart.
Correlation of each gene's copy number with expression. Output of cnv_expression_correlate.py.
Maximum log2 ratio in output. Observed values above this limit will be replaced with this value. [Default: 3.0]
Normal samples (same format as `gene_counts`) to be used as a control to when normalizing and re-centering gene read depth ratios. All filenames following this option will be used.
Directory to write a CNVkit .cnr file for each input sample. [Default: .]
Output file name (summary table).

Skip GC correction.
Skip transcript length correction.
July 2023 cnvkit.py import-rna 0.9.10