Next-Generation Sequencing

Instructor: Phillip Richmond and Oriol Fornés (UBC)

In this workshop we will explore a few different forms of short-read sequencing datasets including ChIP-sequencing and ATAC-sequencing, and where to find them. We will demonstrate how to map and visualize the data against the reference genome, and perform downstream operations such as peak calling. Data will be mapped with the tool BWA, converting formats using samtools, and downstream enrichment/peak calling performed with MACS2.

Target audience: bioinformatics

Duration: 3 hours

Level: beginner / intermediate / expert

Intermediate for following along, beginners are welcome but encouraged to take notes if not confident with the command line.

Prerequisites: Ideally, you should already know Python and the Linux command line (intermediate / proficient). Please use the time before the summer school to find and review basic online Python and bash tutorials. You should also have some knowledge of the human reference genome and have some exposure to genomics, and have a working knowledge of interacting with Cedar compute cluster (SLURM, ssh).

Laptop software: All attendees will need to bring their laptops with wireless access and with a remote SSH (remote login) and SCP/SFTP (remote file transfer) client installed. On Windows laptops we recommend the free edition of MobaXterm; on Mac and Linux laptops no need to install ssh/scp/sftp. Please also install IGV from https://software.broadinstitute.org/software/igv/download.

Not required but ideal: capacity to mount cedar drives onto local desktop (https://www.westgrid.ca/support/sshfs_file_transfer).