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

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 bra

9.2 Read mapping using bra

9.3 SNP calling using varscan

10. Useful references