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.
- RADseq Basics
- RADseq data characteristics
- Algorithmic details of stacks pipeline
Slides for day 1 can be found here.
- 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.
- PCA analysis to detect population structure
Slides for day 3 can be found here.
- We strongly encourage attendees to bring a laptop capable of accessing UCLA’s WiFi.
- stacks – http://catchenlab.life.illinois.edu/stacks/
- snprelate – http://corearray.sourceforge.net/tutorials/SNPRelate/
To be announced
Very nice work! The slides were clear, the explanations were clear, and all of the exercises worked well.
Prerequisites: W1, W2, & W3
or equivalent knowledge
Length: 3 days, 3 hrs per day
Location: Collaboratory Classroom (Boyer Hall, 529)
Seats Available: 28