This repository is intended to document how Salmon transcriptome indices are generated for RNA-seq and scRNA-seq training modules. Currently, this corresponds to our 2019 Houston workshop.
We run all scripts in the Docker container for training (introduced here: AlexsLemonade/RNA-Seq-Exercises).
Note: optparse is not installed on that Docker image but is required to generate the tx2gene files.
Scripts are intended to be run sequentially.