Webinar: Using VICE DESeq2 for RNA Differential Expression Analysis

As RNA sequencing becomes more affordable, differential expression analyses, which offer invaluable insights into intrinsic cellular processes and stochastic gene expression in biological and biomedical research, have become popular. In this webinar, University of Arizona doctoral candidate Sateesh Peri demonstrates how to use two handy new apps in the CyVerse Discovery Environment: the Read Mapping and Transcript Assembly (RMTA) app and the DESeq2 app (RStudio). For anyone doing RNA-Seq differential expression analyses, using these apps in CyVerse's Visual Interactive Computing Environment (VICE) enables you to easily launch RStudio, have quick access to your Data Store files, and interact with your analyses on the fly.

DESeq-2 Video Timestamps - Sateesh Peri

00:00 Introduction
02:30 Webinar Learning Objectives
03:15 RNA Seq overview
06:15 RNA Seq Pipeline in CyVerse
06:55 Step 1: Getting Data
07:40 Step 2: Using the RMTA App
09:35 Step 3: Differential Expression analysis using DESeq-2 app
10:35 Pipeline demo using test data
25:15 Saving outputs
28:00 Questions & Answers
31:41 End

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Still have questions?

This material is based upon work supported by the National Science Foundation under Grant Nos. DBI-0735191, DBI-1265383, and DBI-1743442.

[hannahramcharan]

I have been looking for a tutorial like this for a long time! SO GLAD to have come across this one. Explains very simply and nicely.

[johirislam]

How can i find the common DEG from two dataset of GEO in R languages.Suppose one dataset contain 170 DEG and the other dataset contain 83.Now i want to find the similiar DEG from this two dataset.

[imanemessak]

could you share that Deseq2_script.r script that you used please ?

[arushishrivastava]

Hi, Can u please share the feature_count.txt

[Gbemi]

I feel you need to re-edit the code because you will need to relevel your factor so that the control can be used as a reference because the way you did it in this video means that the drought is used a reference which I think is not correct. We are comparing the drought to the control and as such there is need to used the relevel argument