Overview

The course "High Performance Computing for genomic applications" is organized for the D-BSSE researchers by Scientific IT Services on 23-24 November 2017. The main goal of the course is to increase IT competences of researchers and encourage them to use Euler cluster for bioinformatic analyses: independently or together with a bioinformatician in a co-analysis mode.

Some modules include hands-on exercises, so the participants are expected to bring own laptops. On Friday, Nov 24th there is planned a "hackaton" time slot, when the participants can discuss or work on solutions for their own data analysis issues with the instructors.

Final part of the course is a module "Bioinformatic analysis of immune repertoires from high-throughput sequencing data" delivered by Enkelejda Miho and her colleagues from the Reddy lab.

Application

The classes of the course can be attended or skipped in a "pick-and-mix" mode, depending on the need and skills of the participant, however a registration is required for the full course by filling the form: https://goo.gl/forms/c0ozZyoRpq4x74Kg1

The course is limited to 20 participants, confirmations will be sent after the registration process on first-come-first-served basis.

Location

D-BSSE, Basel

Additional information

Coordination: Michal Okoniewski, Scientific IT Services ETH

Instructors

Michal Okoniewski, Samuel Fux, Manuel Kohler, Enkelejda Miho

Schedule

====> High Performance Computing for genomic applications

Day 1, 23 Nov 2017, Manser room

9:00 - 9:30 Introduction to the Euler cluster and HPC 9:30 -10:15 Linux re-fresh 10:15 -11:00 Basics of shell scripting 11:00 -11:15 Coffee break 11:15- 12:00 LSF queueing system 12:00- 12:30 Genomic formats 12:30- 13:30 Lunch break 13:30- 14:15 Working with genomic data using AWK
14:15- 15:45 Genomic software on the Euler cluster 16:00- 16:15 Coffee break 16:15- 17:30 RNA-seq software tools

Day 2, 24 Nov 2017, RotBlau room

9:00 - 9:30 Workflow orchestration with snakemake - demo 9:30 -10:15 Basics of useful R 10:15 -11:00 Basic R scripts for RNA-seq statistics 11:00 -11:15 Coffee break 11:15 -12:45 Hackaton: participants' own problems and data 12:45 -13:30 Lunch break

====> Bioinformatic analysis of immune repertoires from high-throughput sequencing data 13:30 - 14:00 Introduction 14:00 - 14:45 Preprocessing data 14:45 - 15:00 Coffee break 15:00 - 15:45 Immune repertoire analysis