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| 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 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.
optional arguments:¶
- -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 value in output. Observed values above this limit will be
replaced with this value.
- -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.
