RNA-seq one-command pipeline

I choose a lazy person to do a hard job. Because a lazy person will find an easy way to do it. Bill Gates

This collection of scripts is dedicated to one purpose: align, visualize, and quantify RNA-seq experiments with minimal interaction and using the best practices. The pipeline is implemented in bash and implies the use of a Unix system. It is designed to be applicable to Illumina (paired- and singe-end experiments), as long as colorspace (ABI SOLID) reads.

Prerequisites

The following programs need to be installed and available in the system $PATH variable:

• fastqc
• STAR
• bowtie (v1 for colorspace reads)
• tophat2 (for colorspace reads)
• rsem
• kallisto
• igvtools
• samtools
• Picard tools (as a separate folder)

Configuration file

The following options need to be specified in order for the pipeline to work.

Preparing the reference

This is how you prepare the reference.