Running the pipeline

The easiest way to use the pipeline, is through the genepattern server: module StrandSpecRNAseqEval under RNAseq category. Simply upload your sam file, and press “run”.

Another option is get the scripts, and run them yourself, but please note the following:

1. The scripts are highly customized for yeast data, where since the genome is small, I can load it all to memory, and run all analysis easily.

2. The scripts are written using Matlab.

3.I imagine you come from a computational background, so you can take some of these methods and implement them differently, but just wanted you to be aware of this major issue.

if you are aware of both these issues, and you are still interested in acquiring the scripts, you can download them.