RNA-Seq analysis workflow

Installation

git clone https://github.com/tobiasrausch/RNAseq.git

cd RNAseq

make all

If one of the above commands fail your operating system probably lacks some build essentials. These are usually pre-installed but if you lack them you need to install these. For instance, for Ubuntu this would require:

apt-get install build-essential g++ git wget unzip

Prerequisites

Download STAR GRCh37.75 genome

cd genome/ && ./starGenome.sh

Download the GTF annotation file

cd gtf/ && ./downloadGTF.sh

Download the 1000 Genomes Reference Panel for allele-specific expression

cd refpanel/ && ./download_1kGP_hg19.sh

RNA-Seq alignment, gene counting and variant calling

To perform alignment, generate browser tracks, and call variants you can use the RNA wrapper script.

./src/rna.sh ERR188040_1.fastq.gz ERR188040_2.fastq.gz HG00096

This script also phases variants against the 1000 Genomes reference panel and generates an allele-specific count table.

Example Workflow

To run an entire sample from the gEUVADIS data set

cd example/ && ./gEUVADIS.sh