Assemble the transcripts from RNA-seq read alignments using Cufflinks.
This App assembles transcripts for a given sample or a sample set using Cufflinks and generates an Expression object for each individual sample and an ExpressionSet object for the sample set. The user can view the relative abundances of the assembled transcripts in a histogram, also generated by this App.
It accepts aligned RNA-seq reads from aligners such as Bowtie2, TopHat2, or HISAT2 and assembles the alignments into a parsimonious set of transcripts. It then estimates the relative abundances of these transcripts based on how many reads support each one, taking into account biases in library preparation protocols.
This App also provides the normalized expression matrices which contain the abundance of each transcript expressed in fragments per kilobase of exon per million fragments mapped (FPKM) and transcripts per million (TPM). The FPKM Histogram tab in the Cufflinks table displays the abundance of normalized gene expression value log2(FPKM+1) whereas the TPM Histogram tab displays the abundance of normalized gene expression value log2(TPM+1).
NOTE: This App is one of the steps in the Transcriptomics and Expression Analysis Workflow in KBase, however it can also be run as a standalone for one or more RNA-seq samples.
Team members who developed & deployed algorithm in KBase: Srividya Ramakrishnan, Sunita Kumari, Shinjae Yoo, Priya Ranjan, Jim Thomason, and Vivek Kumar. For questions, please contact us.
- 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
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