Web Portal for Next Generation RNA-seq Sequence Computation and Analysis for Agricultural Animal Species

In order to address the computational challenges in RNA-seq data analysis, especially for researchers in the field of agriculturally important animal studies, we developed a bioinformatics web portal, which offers integrated workflows for RNA-seq NGS data computation and analysis.

These workflows can perform end-to-end computational analysis, including sequence QC, reads mapping, transcriptome assembly and reconstruction and quantification, differential analysis, visualization and so on. One workflow mainly utilizes Tophat2, Cufflink, Cuffmerge and Cuffdiff suite of tools. Another workflow deploys Trinity for de novo assembly and uses RSEM for transcript quantification. Another workflow uses STAR and RSEM combination for computation. For all the workflows, the server supports analysis for multiple samples and multiple groups of samples and performs differential analysis between samples or groups, all in a single job submission. The server currently supports chicken, cow, duck, goat, guinea pig, horse, rabbit, sheep, turkey, as wells as c. elegan, fruit fly, human and yeast. The calculated results are available for download and post analysis.

The portal is implemented with several state-of-the-art HPC, workflow and web development software tools including Galaxy, StarCluster, OGS/GE utilizing modern scalable cloud compute and storage sources from AWS.

This demo will cover several end-to-end RNA-seq analysis projects. The demo includes uploading data files, choosing reference genomes, defining groups (e.g. case vs control), running the full workflow, downloading and visualizing results and post analysis.

The RNA-seq portal is freely available from http://weizhongli-lab.org/RNA-seq.