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Intro to DESeq2 Tutorial


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:


Obtain the starting dataset.

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


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.


Open RStudio using

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

wiki2016deseq2.txt · Last modified: 2017/11/30 09:06 by erin