NSCI 580A3

Instructors
Tai Montgomery
Erin Nishimura

wiki2016deseq2

Intro to DESeq2 Tutorial

Reference

It is easy to follow the DESeq2 instructions even if you are not very familiar with R. Most of the commands in the .R script we'll use today are verbatim taken from the Vignette:

• Most recent vignettes are always linked to the DESeq2 webpage under “Documentation”;

Dataset

Obtain the starting dataset.

$cd$ cp -R /home/erin/04_deseq_demo

Explore

Explore the acquired directory.

Common pitfall When making metadata files, it is often useful to use excel. However, be careful with excel. Many errors can happen. Genes names jun-1 will change to JUNE-01. Also, tab and return characters will often be saved strangely. To avoid issues, try to open txt documents in excel using the import function and switch any text columns from general to text format. Also, to avoid retaining weird carriage returns or extra white space, you can copy excel spreadsheets into TextWrangler and save them as files there.

RStudio

Open RStudio using http://rna.biology.colostate.edu:8787

Let's open the R script ~/04_deseq_demo/171130_wtVMut_DESeq2.R