GVL RNA-seq Differential Gene Expression Advanced Tutorial

RNAseq Differential Gene Expression Advanced tutorial

This tutorial runs on the GVL Galaxy Tutorial Server, a public Galaxy server specifically for learning bioinformatics analysis.

In this tutorial we compare the performance of three statistically-based differential expression tools:

Needed Tools

This tutorial runs on the GVL Galaxy Tutorial Server. All needed tools are on the server.

Datasets

"The data for this tutorial is from the paper, A comprehensive comparison of RNA-Seq-based transcriptome analysis from reads to differential gene expression and cross-comparison with microarrays: a case study in Saccharomyces cerevisiae, by Nookaew et al. which studies S.cerevisiae strain CEN.PK 113-7D (yeast) under two different metabolic conditions: glucose-excess (batch) or glucose-limited (chemostat). The RNA-Seq data has been uploaded in NCBI, short read archive (SRA), with accession SRS307298. There are 6 samples in total having two treatments with three biological replicates each. The data is paired-end. Batch: Batch1 = SRR453566 , Batch2 = SRR453567, Batch3 = SRR453568 Chemostat: Chem1 = SRR453569, Chem2 = SRR453570, Chem3 = SRR453571 "

Needed datasets exist in Shared Libraries on the server, and are also available via URL.