QuickRNASeq – Guide For Pipeline Implementation And For Interactive Results Visualization

Sequencing of transcribed RNA molecules (RNA-seq) has been used wildly for studying cell transcriptomes in bulk or at the single-cell level and is becoming the de facto technology for investigating gene expression level changes in various biological conditions, on the time course, and under drug treatments. Furthermore, RNA-Seq data helped identify fusion genes that are related to certain cancers. Differential gene expression before and after drug treatments provides insights to mechanism of action, pharmacodynamics of the drugs, and safety concerns. Because each RNA-seq run generates tens to hundreds of millions of short reads with size ranging from 50bp-200bp, a tool that deciphers these short reads to an integrated and digestible analysis report is in high demand.

QuickRNASeq is an application for large-scale RNA-seq data analysis and real-time interactive visualization of complex data sets. This application automates the use of several of the best open-source tools to efficiently generate user-friendly, easy to share, and ready to publish reports. The visualization features of the application have been further improved since its first publication in early 2016. The original QuickRNASeq publication provided details of background, software selection, and implementation. Here, researchers from Pfizer Worldwide R&D outline the steps required to implement QuickRNASeq in the user’s own environment, as well as demonstrate some basic yet powerful utilities of the advanced interactive visualization modules in the report.

Interactive plots from QuickRNASeq report

rna-seq

Figures (a, b, c) can be retrieved by clicking on the pointing hands as shown in figure 1d. On any of these interactive plots, mouse over each sample displays associated sample QC metrics. (a) Read mapping summary in the expanded display mode. (b) SNP concordance matrix of 48 samples from 5 donors. Samples from the same donor should be highly concordant. (c) Gene expression chart, which shows the number of genes past various expression thresholds. (d) Center portion of the QuickRNASeq report. (e) Parallel plot linking multiple QC measures for the same samples plus table of multi-dimensional QC measures.

Availability – QuickRNASeq (5) is available from sourceforge: https://sourceforge.net/projects/quickrnaseq.

He W, Zhao S, Zhang C, Vincent MS, Zhang B. (2017) QuickRNASeq: Guide For Pipeline Implementation And For Interactive Results Visualization. bioRXiv [epub ahead of print]. [abstract]

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