---
name: "cnvkit-import-rna"
section: "1"
platform: "linux"
package: "cnvkit"
version: "0.9.12-1"
release: "Debian 13 (Trixie)"
platforms: ["linux"]
url: "https://new.carta.tech/cnvkit-import-rna"
---

# cnvkit-import-rna(1)

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

## NAME

cnvkit\_import-rna - Convert a cohort of per-gene log2 ratios to CNVkit .cnr format.

## DESCRIPTION

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 \[FILES ...\]

### positional arguments:

- FILES

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

### options:

- **-h**, **--help**

  show this help message and exit

- **-f** NAME, **--format** NAME

  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).

- **-g** FILE, **--gene-resource** FILE

  Location of gene info table from Ensembl BioMart.

- **-c** FILE, **--correlations** FILE

  Correlation of each gene's copy number with expression. Output of cnv\_expression\_correlate.py.

- **--max-log2** FLOAT

  Maximum log2 ratio in output. Observed values above this limit will be replaced with this value. \[Default: 3.0\]

- **-n** NORMAL \[NORMAL ...\], **--normal** NORMAL \[NORMAL ...\]

  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.

- **-d** PATH, **--output-dir** PATH

  Directory to write a CNVkit .cnr file for each input sample. \[Default: .\]

- **-o** FILE, **--output** FILE

  Output file name (summary table).

### To disable specific automatic bias corrections:

- **--no-gc**

  Skip GC correction.

- **--no-txlen**

  Skip transcript length correction.