Workshop Description

Restriction site Associated DNA Sequencing (RAD-Seq) sequences short regions immediately flanking restriction sites. RAD-Seq enables cost-effective marker discovery and genotyping of hundreds of thousands of genetic markers in hundreds of samples in ANY species, with or without a reference genome. This three-day workshop will practice hands-on analysis of RAD-Seq data. We will use popular stacks pipeline (http://catchenlab.life.illinois.edu/stacks/) to de novo assemble RAD loci for species lacking a reference genome.

Day 1

  • RADseq Basics
  • RADseq data characteristics
  • Algorithmic details of stacks pipeline

Slides for day 1 can be found here.

Day 2

  • Run the stacks pipeline from raw reads to de novo assemble RAD tag loci.
  • Apply various filters, call variants and estimate summary statistics of genetic variation.

Slides for day 2 can be found here.

Day 3

  • PCA analysis to detect population structure

Slides for day 3 can be found here.

Technical Requirements

Instructor

To be announced

Reviews

It was very good practical workshop. Thank you!
Spring 2017 Student

Very nice work! The slides were clear, the explanations were clear, and all of the exercises worked well.

Spring 2017 Student

Workshop Details

Prerequisites: W1, W2, & W3
or equivalent knowledge
Length: 3 days, 3 hrs per day
Level: Intermediate
Location: Collaboratory Classroom  (Boyer Hall, 529)
Seats Available: 28

Winter 2019 Dates

Sorry! Will return in Spring 2019.