sara

semi automatic RNA-Seq analysis

This repository contains a workflow to performs a RNA-Seq analysis created by Laise de Moraes and Joyce Silva (FIOCRUZ-IGM). This README is also available in brazilian portuguese by click here.

Setting up the pipeline

Download and install the pipeline from the GitHub repo:

git clone --recursive https://github.com/khourious/sara.git; cd sara
chmod 700 -R INSTALL
bash INSTALL

How to use the sara

It is necessary to create the CSV sample sheet. You need create in SHEETS directory.

The csv file name corresponds to the library name and contains in the first line: xxx,xxx,xxx and the next lines: xxxxxxxxxxxxxxxxxxxxxxxxxxxxx -- ATTENTION: NO HEADER!!

xxx,xxx,xxx

semi automatic RNA-Seq analysis

Usage: sara -c <config file name>

-c  Name of CSV file that contains the list of the softwares and the experimental groups.
-t  Max number of threads (default: all cores).