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


usage: cnvkit 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 ...]

positional arguments:

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
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).

To disable specific automatic bias corrections:

Skip GC correction.
Skip transcript length correction.
September 2022 cnvkit import-rna 0.9.9