Broad instructors gave a Terra workshop in collaboration with EnCODE on May 21, 2020. All materials can be found here.
This tutorial uses the Terra platform to compare two H3K27ac ChIP-Seq profiles (tracks) from ENCODE and identify regions where they are different. After locating ENCODE datasets of interest, you will process them in a Terra workspace using a WDL workflow that generates PBS (Probability of Being Signal) scores for genome-wide, 5 kb bins. The PBS values will then be analyzed in a Jupyter Notebook, allowing you to easily identify 5 kb regions of interest and to compare multiple datasets regardless of read depth and peak calling. Finally, you will visualize the interesting 5 kb regions by importing tracks to the Integrated Genomics Viewer (IGV).
Tutorial part 1: [pdf]
Tutorial part 2: [pdf]