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Day 3: Cluster Usage and Data Transfer Short-Read Workshop 2018

Welcome to Day 3 of the Short-Read Sequencing Analysis Workshop. The videos for Day 3 will serve as an introduction to compute clusters and how to work on them. Jobs are submitted to the cluster, jobscripts to perform this will be introduced, as well as calling modules to work with specific programs. Transferring files to/from the cluster, and downloading files from the internet will also be discussed. For the in-class portion of Day 3 we will walk through some practical examples of submitting jobs on the cluster and transferring/downloading data. Additionally we will review the error and log files and how to use them for troubleshooting failed jobs. After this day you should have the basic skills necessary to perform the different analysis pipelines we will be performing throughout the remainder of the workshop.


Videos for Day 3:

3.1 Intro to Compute Cluster

3.2 LMOD

3.3 Data Transfer

3.4 Slurm basics


Files for Day 3:

Day-3 Cheatsheet



Day 3 Homework:

This is Pacific Theme