RNA Seq on HPC

1. Introduction

1.1 RNA-Seq analysis tools

2. Your environment

3. Your data

4. Quality control

5. Trimming

6. The tuxedo pipeline

6.1 Genome indexing for bowtie

6.2 Read mapping using topcoat

6.3 Transcriptome reconstruction and expression using cufflinks

6.4 Differential Expression using cuffdiff