Align sequencing reads to a reference genome using TopHat2 to identify exon-exon splice junctions.
This App aligns the sequencing reads for a set of two or more samples to a genome using TopHat2 in order to identify splice junctions between exons with the help of Bowtie2 mapping program. Alternatively, if the user has only a single sample of reads or set of reads, this App will take single-end or paired-end library object or reads set instead of a sample set.
In addition, it outputs the Qualimap generated BAM alignment QC report that includes global summary such as total number of mapped reads, mean samples coverage, mean samples GC-content, mean samples mapping quality, and sample statistics for each sample along with PCA and coverage statistics in histograms.
NOTE: This method is one of the steps of the KBase RNA-seq Pipeline , however it can also be run standalone for one or more samples.
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
Related Publications
- 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
- 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
- Langmead B, Trapnell C, Pop M, Salzberg SL (2009) Ultrafast and memory-efficient alignment of short DNA sequences to the human genome. Genome Biology 10:R25. , http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2690996/
- 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/
App Specification:
https://github.com/kbaseapps/kb_tophat2/tree/ca4e61a397646dd2a4051f1e59de22dc95d1eed1/ui/narrative/methods/align_reads_using_tophat2Module Commit: ca4e61a397646dd2a4051f1e59de22dc95d1eed1