CUFFQUANT(1)

👑 CUFFQUANT 👑 — like, the cuffquant(1) page but make it make sense 💖

okay bestie, this is cuffquant, a whole component of the cufflinks suite, and it's a User Command which is giving very much "type it in your terminal and vibe". Let's get into it ✨

---

🌸 NAME 🌸

cuffquant — a component of the cufflinks suite. that's it, that's the name, she's iconic 💅

---

🦋 SYNOPSIS 🦋

<sample2_hits.sam> [... sampleN_hits.sam]

yes bestie, it literally says cuffdiff up there in the synopsis. that's what the page says, i'm not touching it, i don't make the rules 🙈

---

✨ DESCRIPTION ✨

cuffquant v2.2.1 (Debian package) — okay so here's the tea, and it's the most important tea in the whole page:

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

like, you don't hand her one file per sample, you hand her a whole lil comma-separated group chat of replicates. fr fr. 💖

---

💜 General Options 💜

• -o/--output-dir — write all output files to this directory [ default: ./ ] — she dumps everything right here in your current folder unless you tell her otherwise 🫶
• -M/--mask-file — ignore all alignment within transcripts in this file [ default: NULL ] — anything matching this file gets the silent treatment 💀
• -b/--frag-bias-correct — use bias correction - reference fasta required [ default: NULL ] — heads up bestie, you need a reference fasta for this one, no fasta no bias correction, periodt
• -u/--multi-read-correct — use 'rescue method' for multi-reads [ default: FALSE ]
• -p/--num-threads — number of threads used during quantification [ default: 1 ] — give her more threads, she goes faster, main character energy 🔥
• --library-type — Library prep used for input reads [ default: below ] — scroll down for the full list, i gotchu 🌈

---

💅 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 ]
• -v/--verbose — log-friendly verbose processing (no progress bar) [ default: FALSE ] — the way that there is no progress bar when you do this 😭
• -q/--quiet — log-friendly quiet processing (no progress bar) [ default: FALSE ] — also no progress bar, she's just not gonna chat 🍓
• --seed — value of random number generator seed [ default: 0 ]
• --no-update-check — do not contact server to check for update availability [ default: FALSE ] — she won't phone home, lowkey respectful
• --max-bundle-frags — maximum fragments allowed in a bundle before skipping [ default: 500000 ]
• --max-frag-multihits — Maximum number of alignments allowed per fragment [ default: unlim ]
• --no-effective-length-correction — No effective length correction [ default: FALSE ]
• --no-length-correction — No length correction [ default: FALSE ]

---

🔧 Debugging use only 🔧

okay so this section is literally labeled "Debugging use only" — these are not your everyday flags, they're for when things are acting up and you need to poke at the machinery, iykyk 🧚

• --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 🌈

these are your options for --library-type, and remember the default is chilling at the bottom of the list:

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

---

and that's the whole page, bestie!! this was cuffquant version 2.2.1+dfsg.1-9, dated November 2021, and it's the CUFFQUANT(1) manual, slay. go quantify something gorgeous 💖✨🎀🦋🌸💅