A comparative study of RNA-seq analysis strategies

This repository holds the pipeline for simulating RNA-seq analyses published in:

Jänes J, Hu F, Lewin A, and Turro E. A Comparative Study of RNA-Seq Analysis Strategies. Briefings in Bioinformatics, March 2015. doi:10.1093/bib/bbv007.

Obtaining

To download the source code, please use git to download the most recent development tree. Currently, the tree is hosted on github, and can be obtained via:

git clone git://github.com/boboppie/RSSS.git

Usage

1. Download data (see data/README.txt for the details)
2. Install all the pre-required software
3. Set the RSSS_DATA_DIR environment variable to the path containing the Ensembl data
4. Execute run_pipeline.sh with the appropriate options: e.g. run_pipeline.sh -c to compute and visualise transcriptome reconstruction accuracy for varying coverage values, or run_pipeline.sh -s to compare sensitivity and precision values

Contributors

RSSS is made by:

• Fengyuan Hu
• Jürgen Jänes
• Ernest Turro
• Alexandra Lewin

Support

email

Please report any issues or questions by creating a ticket, or by email to fh293@cam.ac.uk.