RNA Seq on HPC

The following Hands-on tutorial is based on the EBI teaching materials from Myrto Kostadima and Remco Loos at https://www.ebi.ac.uk/training/online/

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 tophat

6.3 Transcriptome reconstruction and expression using cufflinks

6.4 Differential Expression using cuffdiff

7. Using STAR for read mapping

7.1 Genome indexing for STAR

7.2 Read mapping using STAR

7.3 Using cuffdiff on STAR mapped reads

8. De novo assembly with Velvet

9. Using bwa for read mapping and SNP calling

9.1 Genome indexing for bwa

9.2 Read mapping using bwa

9.3 SNP calling using varscan

10. Useful references