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/
6.1 Genome indexing for bowtie
6.3 Transcriptome reconstruction and expression using cufflinks
6.4 Differential Expression using cuffdiff
7. Using STAR for read mapping
7.3 Using cuffdiff on STAR mapped reads
8. De novo assembly with Velvet