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Cuffdiff 2

Cuffdiff 2

Cuffdiff 2 is a tool to estimate differential expression at gene and transcript levels. It uses a negative binomial model, normalizes using the relative log expression method implemented in DESeq, Inter-sample normalization method Q, and reports Fragments per kilobase million Reads per million mapped reads (FPKM). Cuffdiff 2 is a part of the Cufflinks suite of tools.


Transcriptomics; RNA splicing; RNA-Seq


  • Operation: RNA-seq time series analysis
  • Input: GFF,GTF,BAM,SAM
  • Output: Gene expression profile, Report
  • Software interface: Command-line user interface
  • Language: C++
  • Operating system: Linux; Mac OS X
  • License: Boost Software License 1.0
  • Cost: Free
  • Version name: 2.2.1
  • Maturity: Mature
  • Credit: US National Institutes of Health (NIH).
  • Contact: Cole Trapnell coletrap _at_ | Cole Trapnell cole _at_ | Adam Roberts adarob _at_ | Julie Donaghey donaghey _at_ | John L Rinn john_rinn _at_ | Lior Pachter lpachter _at_
  • Collection: Cufflinks


Trapnell C, Hendrickson DG, Sauvageau M, Goff L, Rinn JL, Pachter L "Differential analysis of gene regulation at transcript resolution with RNA-seq." Nat Biotechnol. 2013 Jan;31(1):46-53.
PMID: 23222703
PMCID: PMC3869392

Trapnell C, Williams BA, Pertea G, Mortazavi A, Kwan G, van Baren MJ, Salzberg SL, Wold BJ, Pachter L "Transcript assembly and quantification by RNA-Seq reveals unannotated transcripts and isoform switching during cell differentiation." Nat Biotechnol. 2010 May;28(5):511-5.
PMID: 20436464
PMCID: PMC3146043

Roberts A, Pimentel H, Trapnell C, Pachter L "Identification of novel transcripts in annotated genomes using RNA-Seq" Bioinformatics. 2011 Sep 1;27(17):2325-9
PMID: 21697122

Roberts A, Trapnell C, Donaghey J, Rinn JL, Pachter L "Improving RNA-Seq expression estimates by correcting for fragment bias." Genome Biol. 2011;12(3):R22.
PMID: 21410973
PMCID: PMC3129672

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