Bioinformatics sessions: data analysis tools
This is a 3-day workshop.
Target audience: researchers in bioinformatics
Level: beginner
Software: All attendees will need a remote secure shell (SSH) client installed on their computer in
order to participate in the course exercises. On Windows we recommend
the free Home Edition of MobaXterm. On Mac and Linux
computers SSH is usually pre-installed (try typing ssh in a terminal to make sure it is there).
Wednesday June-17
“Short read mapping and visualization: Core aspects of next-generation sequencing data analysis”
with Phillip Richmond
You can find the online slides here. Here is the PDF version.
Today we will be submitting jobs to the reservation on Cedar:
cd ~/scratch
salloc --account=def-training-wa_cpu --reservation=wgss1-wr_cpu --mem-per-cpu=... --time=... <other_flags>
- session opening
- 30-min lecture
- participants watch videos 1 & 2 (~10-15 min each) and complete activities for each; activities will range from 15 min to 45 min depending on skill level
- reconvene, mini check-in
- participants watch video 3, complete activity afterwards
- reconvene, describe homework, close
Thursday June-18
“Building a Reproducible Data Analysis Pipeline”
with Matthew Douglas (Genome Science Center)
You can find the PDF slides here.
- 45-60min presentation + some time for Q&A, no coding for the audience
- based on first-hand experience in several research projects
Friday June-19
“Setting up a bioinformatics pipeline with SnakeMake”
with Brian McConeghy
You can find the PDF slides here. You might also want to check Brian’s materials from 2019 in-person summer school with hands-on examples and the official Snakemake documentation.
- 60min presentation followed by live Q&A