RADCamp NYC 2023 Part II (Bioinformatics)

Day 2 (PM)

Overview of the afternoon activities:

• Small group work focused on the pilot datasets
• Analysis breakout rooms 1
• Coffee Break
• Analysis breakout rooms 2
• Group presentation
• Wrap-up & adjourn

Small group work focused on the pilot datasets

Lead: Isaac (20’)

Break into groups around real data with the intention of running a few analyses, creating some plots and reporting the results to the rest of the group.

• Assign one group member to lead/coordinate analysis and to update the results slides.
• For groups with assemblies that finished running you’ll use the output files in your /scratch/ipyrad-workshop/*_outfiles directory.
• For the groups with assemblies that did not finish running, you will need to attach a data asset which is called *_assembly which contains the complete assembly including outfiles which we have performed in advance.
• Ideally, everyone will run every type of analysis. But there is limited time. So each person will instead choose one analysis to run first, and can do other analyses after if they have time.
• Assign analyses to participants/groups with the plan to complete 2-3 analyses by end of day.

Results should be put in the google slides presentation in the RADCamp google drive folder.

Overview of other available API mode tools

The core analysis tools all have detailed cookbooks available on the ipyrad API analysis tools page.

A couple other cookbooks that are useful for understanding the data but not on that page include:

• Pairwise sharing of present/missing data
• Pairwise genetic distance
• Demographic analysis with the site frequency spectrum & momi2)

Analysis breakout rooms 1

Lead: All (60’)

Instructors will rotate among groups during this time to make sure everyone is making progress.

Coffee break (2:30-3:00)

Analysis breakout room 2 (synthesize the results)

Lead: All (60’)

• Groups meetup, some analyses can continue running. Decide what will finish in time.
• Enter finished results into the slideshow, discuss their meaning together.
• Coordinate on updating the results presentation

Presentation of results of small group analysis

Please update the brief presentation (1-2 slides max) to highlight any interesting results you might have obtained in the Google Drive folder for draft results slides.

Wrap-up & adjourn

• Please take a moment to fill out the RADCamp 2023 Exit Survey
• Thanks for joining us!!!!!!!