CUFFDIFF(1)

📦
version 2.2.1 · 3 versions
, in debian bookworm, ubuntu jammy

💖 CUFFDIFF(1) 💖

okay bestie, gather round, because we're doing cuffdiff — a whole component of the cufflinks suite 🦋 and honestly? it's giving main character energy in the RNA-seq world.

✨ NAME ✨

cuffdiff — component of cufflinks suite 👑

🌸 SYNOPSIS 🌸

cuffdiff [options] <transcripts.gtf> <sample1_hits.sam>
<sample2_hits.sam> [... sampleN_hits.sam]

🎀 DESCRIPTION 🎀

so like, we're on cuffdiff v2.2.1 (Debian package) and here's the lil header it comes with:

-----------------------------

and the actual important bit, no cap:

  • Supply replicate SAMs as comma separated lists for each condition: sample1_rep1.sam,sample1_rep2.sam,...sample1_repM.sam

💅 General Options 💅

  • -o, --output-dir — write all output files to this directory — default: ./ 📁
  • -L, --labels — comma-separated list of condition labels 🏷️
  • --FDR — False discovery rate used in testing — default: 0.05 🎯
  • -M, --mask-file — ignore all alignment within transcripts in this file — default: NULL 🙈
  • -C, --contrast-file — Perform the constrasts specified in this file — default: NULL ⚖️
  • -b, --frag-bias-correct — use bias correction - reference fasta required — default: NULL 🧬
  • -u, --multi-read-correct — use 'rescue method' for multi-reads — default: FALSE 🚑
  • -p, --num-threads — number of threads used during quantification — default: 1 🧵
  • --no-diff — Don't generate differential analysis files — default: FALSE 🚫
  • --no-js-tests — Don't perform isoform switching tests — default: FALSE 🚫
  • -T, --time-series — treat samples as a time-series — default: FALSE ⏰
  • --library-type — Library prep used for input reads — default: below 👇
  • --dispersion-method — Method used to estimate dispersion models — default: below 👇
  • --library-norm-method — Method used to normalize library sizes — default: below 👇

🔥 Advanced Options 🔥

  • -m, --frag-len-mean — average fragment length (unpaired reads only) — default: 200 📏
  • -s, --frag-len-std-dev — fragment length std deviation (unpaired reads only) — default: 80 📐
  • -c, --min-alignment-count — minimum number of alignments in a locus for testing — default: 10 🔢
  • --max-mle-iterations — maximum iterations allowed for MLE calculation — default: 5000 🔁
  • --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 📵
  • --emit-count-tables — print count tables used to fit overdispersion — DEPRECATED ⚠️
  • --max-bundle-frags — maximum fragments allowed in a bundle before skipping — default: 500000 📦
  • --num-frag-count-draws — Number of fragment generation samples — default: 100 🎰
  • --num-frag-assign-draws — Number of fragment assignment samples per generation — default: 50 🎰
  • --max-frag-multihits — Maximum number of alignments allowed per fragment — default: unlim ♾️
  • --min-outlier-p — Min replicate p value to admit for testing — DEPRECATED ⚠️
  • --min-reps-for-js-test — Replicates needed for relative isoform shift testing — default: 3 3️⃣
  • --no-effective-length-correction — No effective length correction — default: FALSE 🚫
  • --no-length-correction — No length correction — default: FALSE 🚫
  • -N, --upper-quartile-norm — Deprecated, use --library-norm-method — DEPRECATED ⚠️
  • --geometric-norm — Deprecated, use --library-norm-method — DEPRECATED ⚠️
  • --raw-mapped-norm — Deprecated, use --library-norm-method — DEPRECATED ⚠️
  • --poisson-dispersion — Deprecated, use --dispersion-method — DEPRECATED ⚠️
bestie the DEPRECATED ones are literally deprecated okay, don't come for me, just use the shiny replacement options like the girlies intended 💅

🐛 Debugging use only 🐛

  • --read-skip-fraction — Skip a random subset of reads this size — default: 0.0 🎲
  • --no-read-pairs — Break all read pairs — default: FALSE 💔
  • --trim-read-length — Trim reads to be this long (keep 5' end) — default: none ✂️
  • --no-scv-correction — Disable SCV correction — default: FALSE 🚫

🌈 Supported library types 🌈

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

🦋 Supported dispersion methods 🦋

blind per-condition poisson pooled (default)

⭐ Supported library normalization methods ⭐

classic-fpkm geometric (default) geometric quartile

and that's the whole vibe, bestie — go quantify some transcripts and slay 💖✨🎀🫶👑

this iconic lil page is brought to you by cuffdiff 2.2.1+dfsg.1-9, dated November 2021 — periodt 💅🌸🦋

📦 where this page comes from