Assemble the transcripts from RNA-seq reads using StringTie
This App assembles transcripts for an individual Alignment or an AlignmentSet using StringTie so that you can view the relative abundances of the assembled transcripts in a histogram.
StringTie is a successor of Cufflinks that is faster and provides more accurate reconstruction of genes and expression level. It accepts aligned RNA-seq reads from HISAT2, TopHat2 or Bowtie2 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.
The StringTie output object contains GTF (transcripts.gtf) and FPKM (genes.fpkm_tracking) files. The GTF file contains annotated transcripts assembled by StringTie whereas the FPKM file provides the normalized expression matrix objects (abundance of each transcript expressed in fragments per kilobase of exon per million fragments mapped (FPKM) and transcripts per kilobase million (TPM)). The StringTie Table Histogram tab displays the abundance of normalized gene expression value in both log2(FPKM+1) and log2(TPM+1).
The StringTie output object can be used to identify differential expression either using DESeq2, Cuffdiff or Ballgown.
This method is one of the steps of the KBase RNA-seq Pipeline , however it can also be run standalone.
Team members who developed & deployed algorithm in KBase: Tianhao Gu, Christopher Henry, Shane Canon, Stephen Chan, Jason Baumohl, Sean McCorkle, Sunita Kumari, Shinjae Yoo, Priya Ranjan, Vivek Kumar
- Pertea M, Pertea GM, Antonescu CM, Chang TC, Mendell JT & Salzberg SL. StringTie enables improved reconstruction of a transcriptome from RNA-seq reads Nature Biotechnology 2015 , http://www.nature.com/nbt/journal/v33/n3/full/nbt.3122.html
- Kim D, Pertea G, Trapnell C, Pimentel H, Kelley R, Salzberg SL (2013) TopHat2: accurate alignment of transcriptomes in the presence of insertions, deletions and gene fusions. Genome Biology. 14:R36 , http://www.genomebiology.com/2013/14/4/R36/abstract
- Trapnell C, Roberts A, Goff L, Pertea G, Kim D, Kelley DR, Pimentel H, Salzberg SL, Rinn JL, Pachter, L (2012) Differential gene and transcript expression analysis of RNA-seq experiments with TopHat and Cufflinks. Nature Protocols, 7(3), 562 578. , http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3334321/
- Trapnell C, Pachter L, Salzberg SL. (2009) TopHat: discovering splice junctions with RNA-Seq. Bioinformatics. Vol 25, 9:1105-1111. , http://bioinformatics.oxfordjournals.org/content/25/9/1105.abstract
- Frazee, A. C., Pertea, G., Jaffe, A. E., Langmead, B., Salzberg, S. L., & Leek, J. T. (2015). Ballgown bridges the gap between transcriptome assembly and expression analysis. Nature Biotechnology, 33(3), 243 246. , http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4792117/
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