RNA-Seq Pipeline

The GDC mRNA-Seq alignment workflow follows the International Cancer Genome Consortium (ICGC) STAR [1] 2-pass RNA-Seq alignment SOP, and is shown below. FastQC and RNA-SeQC are used to collect alignment metrics. Per read group alignment is handled by the STAR aligner internally, and is not reflected explicitly in the diagram.

RNA Alignment Pipeline

RNA Sequence Workflow

The GDC miRNA-Seq alignment and quantification workflow follows the modified TCGA miRNA-Seq workflow developed by the University of British Columbia. The process includes adaptor trimming, BWA alignment, and miRNA profiling. The profiling steps consist of multiple Perl and R scripts to access UCSC and Ensembl databases, annotate mapped reads, quantify miRNA isoforms, and create summary plots.

[1]. Dobin A1, Davis CA, Schlesinger F, Drenkow J, Zaleski C, Jha S, Batut P, Chaisson M, Gingeras TR. Bioinformatics. 2013 Jan 1;29(1):15-21. doi: 10.1093/bioinformatics/bts635. Epub 2012 Oct 25. STAR: ultrafast universal RNA-seq aligner.