Identify differential expression in the gene and transcript expression level using Cuffdiff.
This App takes as input the read alignments and assembled transcripts corresponding to two or more conditions and reports genes and transcripts which are differentially expressed under different conditions. More specifically, it generates a set of differential expression matrices for selected or all pairwise condition combinations as chosen by the user.
The App also generates a zipped output file that contains FPKM tracking, count tracking, read group tracking and differential expression files for transcripts, CDSes, and genes for each condition.
The Cuffdiff output can be further analyzed as up and down regulated features and associated expression matrices by the downstream App Create Up/Down Regulated FeatureSet and ExpressionMatrix .
Related Publications
- Kim D, Pertea G, Trapnell C, Pimentel H, Kelley R, Salzberg SL. TopHat2: accurate alignment of transcriptomes in the presence of insertions, deletions and gene fusions. Genome Biology. 2013;14: R36. doi:10.1186/gb-2013-14-4-r36 , https://genomebiology.biomedcentral.com/articles/10.1186/gb-2013-14-4-r36
- Langmead B, Trapnell C, Pop M, Salzberg SL. Ultrafast and memory-efficient alignment of short DNA sequences to the human genome. Genome Biol. 2009;10: R25. doi:10.1186/gb-2009-10-3-r25 , https://genomebiology.biomedcentral.com/articles/10.1186/gb-2009-10-3-r25
- Trapnell C, Pachter L, Salzberg SL. TopHat: discovering splice junctions with RNA-Seq. Bioinformatics. 2009;25: 1105 1111. doi:10.1093/bioinformatics/btp120 , https://academic.oup.com/bioinformatics/article/25/9/1105/203994
- Trapnell C, Roberts A, Goff L, Pertea G, Kim D, Kelley DR, et al. Differential gene and transcript expression analysis of RNA-seq experiments with TopHat and Cufflinks. Nat Protoc. 2012;7: 562 578. doi:10.1038/nprot.2012.016 , https://www.nature.com/articles/nprot.2012.016
App Specification:
https://github.com/kbaseapps/kb_cufflinks/tree/d2a31f34c14aa9536a3776e7a6f9c28687ad638c/ui/narrative/methods/run_CuffdiffModule Commit: d2a31f34c14aa9536a3776e7a6f9c28687ad638c