RNA-Seq Support Scripts

Warning: Work in progress. Not yet ready for use in research.

RNA Systems Biology Lab at BioISI

Author: Gil Oliveira, PI: Margarida Gama-Carvalho

A collection of scripts to support RNA-Seq analysis workflows.

Install

Clone this repository to a convenient directory, such as /data/rna-scripts, and then cd into the project's root.

git clone https://github.com/GamaPintoLab/RNA-Seq.git /data/rna-scripts`
cd /data/rna-scripts

Then, to install, run:

make

or, alternatively, make install. This will install the scripts locally to the current user. Run command as root to install system-wide.

Update

Open a console session in the root of this project, then run:

make update

This will fetch the latest changes from the repository and update the local installation of the scripts.

Learn

This project is composed of 4 scripts, you should consult their respective documentations prior to using them, which you can find in the docs folder. Good practice also mandates that you audit the source code first, which you can find in the src folder.

Prepare

SSH, which you'll be using to connect to the server, requires you maintain your connection to the server throughout the script's execution. If your connection drops, or you put your PC do sleep, the process will interrupt. That's far from ideal when dealing with pipelines (such as this one) that can last for a few hours, so, it is highly recommended that you use a terminal multiplexer, like tmux to run these scripts. For a primer on how to use it and why it's so important, be sure to read prep.md before continuing.

Run

Most of these scripts can be run in 2 modes:

• Interactive
• Non-interactive

Interactive mode prompts the user for the variables it relies upon. You can use your arrow keys and Enter to select the project you're working on and type the parameters when you're asked for them.

Non-interactive mode helps you integrate the scripts into an automated pipeline, or allows you to change parameters that aren't prompted in interactive mode. You set the parameters using runtime flags after the script name. To learn which flags are accepted, you can use the -h (help) flag and the shell will return a list of available runtime flags.

Once you've installed the scripts, you can simply call them using their name:

dataprep
genomefetch
readcount
seqalign