table of contents
| CNVKIT_IMPORT-RNA(1) | User Commands | CNVKIT_IMPORT-RNA(1) |
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.
| July 2023 | cnvkit.py import-rna 0.9.10 |