CUFFLINKS(1)

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

okay bestie, pull up a chair, because this is the cufflinks manual page — yes, the one from User Commands, and yes, I'm gonna walk you through it like we're texting at 2am. 🫶

✨ NAME ✨

cufflinks — it's a component of the cufflinks suite. that's the whole vibe. it does one job and it does it iconically. 💅

🌸 SYNOPSIS 🌸

cufflinks [options] <hits.sam>

that's it. options first, then your .sam file, and she's ready to go. periodt. ⭐

🦋 DESCRIPTION 🦋

so here's the tea: this is cufflinks v2.2.1 and she's linked against Boost version 107400. no cap.

👑 General Options:

  • -o, --output-dir — every single output file goes into this directory. [ default: ./ ] 🎀
  • -p, --num-threads — how many threads get to help out during the analysis. [ default: 1 ] ⚡
  • --seed — the value of the random number generator seed. [ default: 0 ] 🎲
  • -G, --GTF — quantitate against reference transcript annotations. 🧬
  • -g, --GTF-guide — use the reference transcript annotation to guide the assembly. like a lil GPS but for transcripts. 🗺️
  • -M, --mask-file — ignore all alignment within transcripts in this file. 🙈
  • -b, --frag-bias-correct — use bias correction — heads up, a reference fasta is required for this one. [ default: NULL ]
  • -u, --multi-read-correct — use the 'rescue method' for multi-reads (it's more accurate, bestie). [ default: FALSE ] 💖
  • --library-type — the library prep used for input reads. [ default: below ] 👇
  • --library-norm-method — the method used to normalize library sizes. [ default: below ] 👇

💜 Advanced Abundance Estimation Options:

  • -m, --frag-len-mean — average fragment length (unpaired reads only, just so u know). [ default: 200 ]
  • -s, --frag-len-std-dev — fragment length std deviation (again, unpaired reads only). [ default: 80 ]
  • --max-mle-iterations — the maximum iterations allowed for MLE calculation. [ default: 5000 ] 🔁
  • --compatible-hits-norm — count hits compatible with reference RNAs only. [ default: FALSE ]
  • --total-hits-norm — count all hits for normalization. [ default: TRUE ]
  • --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 ]
  • --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 instead. [ DEPRECATED ] 💀
  • --raw-mapped-norm — deprecated, use --library-norm-method instead. [ DEPRECATED ] 💀
bestie the deprecated ones are deprecated fr fr. they still show up but you should be using --library-norm-method. don't be messy. 🙈

🌈 Advanced Assembly Options:

  • -L, --label — assembled transcripts get this ID prefix. [ default: CUFF ] 🏷️
  • -F, --min-isoform-fraction — suppress transcripts below this abundance level. [ default: 0.10 ]
  • -j, --pre-mrna-fraction — suppress intra-intronic transcripts below this level. [ default: 0.15 ]
  • -I, --max-intron-length — ignore alignments with gaps longer than this. [ default: 300000 ]
  • -a, --junc-alpha — alpha for the junction binomial test filter. [ default: 0.001 ]
  • -A, --small-anchor-fraction — percent read overhang taken as 'suspiciously small'. [ default: 0.09 ] 👀
  • --min-frags-per-transfrag — minimum number of fragments needed for new transfrags. [ default: 10 ]
  • --overhang-tolerance — number of terminal exon bp to tolerate in introns. [ default: 8 ]
  • --max-bundle-length — maximum genomic length allowed for a given bundle. [ default: 3500000 ]
  • --max-bundle-frags — maximum fragments allowed in a bundle before skipping. [ default: 500000 ]
  • --min-intron-length — minimum intron size allowed in genome. [ default: 50 ]
  • --trim-3-avgcov-thresh — minimum avg coverage required to attempt 3' trimming. [ default: 10 ]
  • --trim-3-dropoff-frac — fraction of avg coverage below which to trim the 3' end. [ default: 0.1 ]
  • --max-multiread-fraction — maximum fraction of allowed multireads per transcript. [ default: 0.75 ]
  • --overlap-radius — maximum gap size to fill between transfrags (in bp). [ default: 50 ]

🧚 Advanced Reference Annotation Guided Assembly Options:

  • --no-faux-reads — disable tiling by faux reads. [ default: FALSE ]
  • --3-overhang-tolerance — overhang allowed on the 3' end when merging with reference. [ default: 600 ]
  • --intron-overhang-tolerance — overhang allowed inside a reference intron when merging. [ default: 30 ]

🍓 Advanced Program Behavior Options:

  • -v, --verbose — log-friendly verbose processing (no progress bar, sorry to the bar stans). [ default: FALSE ]
  • -q, --quiet — log-friendly quiet processing (also no progress bar). [ default: FALSE ] 🤫
  • --no-update-check — do not contact the server to check for update availability. [ default: FALSE ] 📵

⭐ Supported library types:

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

👑 note that fr-unstranded is the default one, k?

💅 Supported library normalization methods:

classic-fpkm

that's the whole list. one icon. she ate. 🔥

and that's the page bestie!! this was cufflinks version 2.2.1+dfsg.1-9, dated November 2021 — mwah, sending u off with a kiss, go assemble something gorgeous 🫶✨🎀

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