CUFFNORM(1)

💖 NAME 💖

okay so hi bestie, welcome 🫶 you've found cuffnorm — she's a component of the cufflinks suite. that's literally the whole name section. short, sweet, iconic. 💅

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✨ SYNOPSIS ✨

cuffnorm [options] <transcripts.gtf> <sample1_expr.cxb> <sample2_expr.cxb> [... sampleN_expr.cxb]

so you hand her some <transcripts.gtf>, then a whole lineup of .cxb files — <sample1_expr.cxb>, <sample2_expr.cxb>, all the way to <sampleN_expr.cxb>. plus [options], obviously, because options are the moment. 💖

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🌸 DESCRIPTION 🌸

this is cuffnorm v2.2.1 (Debian package) -----------------------------

and here's the tea 🍓 — you supply replicate CXB files as comma separated lists for each condition, like this:

sample1_rep1.cxb,sample1_rep2.cxb,...sample1_repM.cxb

so all your reps for one condition get smooshed into one comma-y lil list. no cap. 💅

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💅 General Options 💅

• -o, --output-dir — write all output files to this directory. default: ./ (aka right here, right now, bestie 🏠)
• -L, --labels — a comma-separated list of condition labels 🏷️
• --norm-standards-file — housekeeping/spike genes to normalize libraries. default: NULL
• -p, --num-threads — number of threads used during quantification. default: 1 🧵
• --library-type — library prep used for input reads. default: below (yes, literally the word "below" — go peek at the supported library types list further down 👀)
• --library-norm-method — method used to normalize library sizes. default: below (again — scroll down to the normalization methods list, bestie ⬇️)
• --output-format — format for output tables. default: below (yep, "below" again — the output formats list is down there ✨)

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🔥 Advanced Options 🔥

• --compatible-hits-norm — count hits compatible with reference RNAs only. default: TRUE ✅
• --total-hits-norm — count all hits for normalization. default: FALSE
• -v, --verbose — log-friendly verbose processing (no progress bar). default: FALSE 🗣️
• -q, --quiet — log-friendly quiet processing (no progress bar). default: FALSE 🤫
• --seed — value of random number generator seed. default: 0 🎲
• --no-update-check — do not contact server to check for update availability. default: FALSE 📵

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🦋 Supported library types 🦋

• ff-firststrand
• ff-secondstrand
• ff-unstranded
• fr-firststrand
• fr-secondstrand
• fr-unstranded (default) 👑
• transfrags

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🌈 Supported library normalization methods 🌈

• classic-fpkm
• geometric (default) 👑
• geometric
• quartile

not me pointing out that geometric is in there twice 🙈 i'm literally just the messenger, i'm reading it exactly how it's written, bestie. no edits, no notes. 💖

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⭐ Supported output formats ⭐

• cuffdiff
• simple-table (default) 👑

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and that's the whole page, periodt. 🎀 this was cuffnorm version 2.2.1+dfsg.1-9, and the page is dated November 2021 — so go normalize something and slay, you've got this fr fr. 💜✨