Workshop Description
This workshop aims to provide skills needed to address experimental reproducibility, sequencing depth, data reporting and quality assessment of ChIP-seq data. Students will have opportunities to practice hands-on with state-of-the-art analytical tools.
Day 1
- Cross-correlation analysis and ENCODE QC with SPP
- BigWig tracks with defined resolution and normalization using
- Homer/UCSC tools, and visualization with IGV
- Peak calling with MACS2
Slides for all 3-days can be found here.
Day 2
- QC of replicates with ENCODE’s IDR
- Differential peak calling with MAnorm
- Location annotation with NGSPLOT
Slides for all 3-days can be found here.
Day 3
- Functional annotation with GREAT
- Motif analysis with HOMER
- Command-line tools to work more efficiently
- Open Q&A
Slides for all 3-days can be found here.
Technical Requirements
- Attendees are required to have a Hoffman2 account. To apply for an account, click here. UCLA participants who lack a faculty sponsor and non-UCLA participants may apply for a temporary Hoffman2 account, requesting sponsorship from Collaboratory Workshops.
- We strongly encourage attendees to bring a laptop capable of accessing UCLA’s WiFi.
Instructor
To be announced
Reviews
This was a great workshop that shows the various steps and options for representing and analyzing ChIP-seq data. The outline of the overall workshop made sense and provided me with a lot of information to try. Thanks!
I was glad that we went over QC methods and tools.
This is a good workshop for biologists to understand the analysis process of ChIP-seq data.
Workshop Details
Prerequisites: W1, W2, W& 4
Length: 3 days, 3 hrs per day
Level: Introductory
Location: Collaboratory Classroom (Boyer Hall, 529)
Seats Available: 15
Winter 2019 Dates
Sorry! Will return in Spring 2019.