CNVKIT_IMPORT-RNA(1)

💅 NAME 💅

cnvkit_import-rna — bestie, this is the glow-up machine that takes a whole cohort of per-gene log2 ratios and converts them into CNVkit .cnr format. No cap. ✨

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🦋 DESCRIPTION 🦋

okay so first things first, here's how you actually call it:

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 ...]

that's the whole vibe. now let's break it down piece by piece 🫶

🌸 positional arguments 🌸

• FILES — these are your tabular files, the ones with Ensembl gene ID and the number of reads mapped to each gene. you can get them from RSEM or literally any other transcript quantifier, we're not picky 💖

🎀 options 🎀

• -h, --help — shows this help message and then dips. iconic behaviour honestly.
• -f NAME, --format NAME — tells the tool what the input format name is. two choices, pick your fighter:
  • 'rsem' for RSEM gene-level read counts, aka the *_rsem.genes.results files
  • 'counts' for generic 2-column gene IDs and their read counts (like, say, TCGA level 2 RNA expression)
• -g FILE, --gene-resource FILE — where the gene info table from Ensembl BioMart is hiding. yes it's required, yes you need it, no you cannot skip it 👑
• -c FILE, --correlations FILE — the correlation of each gene's copy number with expression. this is the output of cnv_expression_correlate.py. it's giving very much "bring your own homework".
• --max-log2 FLOAT — the maximum log2 ratio allowed in the output. if any observed values go above this limit they get replaced with this value instead. sneakily firm. [Default: 3.0]
• -n NORMAL [NORMAL ...], --normal NORMAL [NORMAL ...] — normal samples (same format as gene_counts) used as a control when normalizing and re-centering gene read depth ratios. heads up: every single filename following this option gets used, so don't just keep typing filenames after it unless you mean it 😭
• -d PATH, --output-dir PATH — the directory where a CNVkit .cnr file gets written for each input sample. [Default: .]
• -o FILE, --output FILE — the output file name for the summary table.

✨ to disable specific automatic bias corrections ✨

(yes, this is its own little section, because sometimes you just want to turn the autopilot off)

• --no-gc — skips GC correction. bye girl 👋
• --no-txlen — skips transcript length correction. also bye 👋

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💀 quick vibe check: -g is not optional. do not forget the gene resource. do not show up to the group chat complaining that it didn't work when you forgot -g. i love you but i will not be doing that.

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and that's the whole page, bestie!! 🍓 this was cnvkit.py import-rna version 0.9.10, dated July 2023, and yeah that's genuinely it — go convert some ratios, you're gonna slay 💖✨🎀🦋🌸💅🫶