Using Cloud Computing for RNA-seq: Tutorial

Stuart Brown
NYU Center for Health Informatics & Bioinformatics

The full tutorial is available in a PDF file. To view the PDF, click here.

RNA-seq Measures Gene Expression

• Takes advantage of the rapidly dropping cost of Next-Generation DNA sequencing
• Measures gene expression in true genome-wide fashion (all the RNA)
• Also enables detection of mutations (SNPs), alternative splicing, allele specific expression, and fusion genes
• More accurate and better dynamic range than Microarray
• Can be used to detect miRNA, ncRNA, and other non-coding RNA

RNA-seq is very compute intensive

• Billions of reads
• Large file sizes (tens of GB)
• Alignment to complete reference genomes
• Spliced alignment
• Like most genomics research institutes, NYU has purchases substantial High Performance Computing (HPC) resources to support our NGS lab.
  • Cluster of servers
  • Machines with large amount of RAM
  • Data storage and backup system

Cloud = Renting Computers

• Instead of buying a High Performance Computing system, rent time on one from a vendor
• Amazon EC2 has simplified this process
• Scalable: Pay just for the computing you need, only when you need it.
• Also has benefits to move and share data among many users at different institutions with different security policies

The rest of the tutorial is available in a PDF file. To view the PDF, click here.