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
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. https://doi.org/10.1038/nbt.2450
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. https://doi.org/10.1038/nbt.1621
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 https://doi.org/10.1093/bioinformatics/btr355
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. https://doi.org/10.1186/gb-2011-12-3-r22
PMID: 21410973
PMCID: PMC3129672
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