RNA Seq Data Analysis copy

This page contains content taken directly from the Biostars Handbook by Istvan Albert.

Remember to activate the bioinformatics environment.

conda activate bioinfo

Install the statistical packages we will need for the analysis,

curl http://data.biostarhandbook.com/books/rnaseq/code/install-conda.txt | xargs conda install -y

and modify the permissions.

chmod +x ~/bin/*.r

Temporary note for MacOS only. Due to an installation error by conda the wrong version of a package is installed. On MacOS a temporary fix is to run:

conda install -y libopenblas==0.3.7

We have written scripts that make use of several different R based methods. We have devoted a substantial effort to standardizing both the usage and the results produced by these different methods.

To make these scripts universally accessible and simpler to use, we recommend saving them into the ~/bin folder and making them executable. You can achieve that from the command line with:

mkdir -p ~/bin

# Download the scripts into the ~/bin folder.
curl http://data.biostarhandbook.com/books/rnaseq/code/deseq1.r > ~/bin/deseq1.r
curl http://data.biostarhandbook.com/books/rnaseq/code/deseq2.r > ~/bin/deseq2.r
curl http://data.biostarhandbook.com/books/rnaseq/code/edger.r > ~/bin/edger.r
curl http://data.biostarhandbook.com/books/rnaseq/code/heatmap.r > ~/bin/heatmap.r

# Make them executable
chmod +x ~/bin/*.r

Test that the code works by typing:

deseq1.r

it should print something similar:

Error: The experimental design must be specified as NxM
Execution halted

Run the edger.r script

cat counts.txt | Rscript ~/bin/edger.r 3x3 > output.txt

both deseq1.r and deseq2.r give error messages.

cat norm-matrix-edgeR.txt | Rscript draw-heatmap.r > output.pdf

Open "output.pdf" with a pdf reader such as Acrobat.

It should look something like this.

Screen Shot 2020-07-16 at 10 42 24 AM