'>Workshop Description (Intermediate Course)
This workshop aims to provide skills needed to address principles of the assay, quality assessment, sequencing depth, data processing and functional downstream analyses of ChIP-seq datasets. Students will have opportunities to practice hands-on with state-of-the-art analytical tools.
Workshop Topics
Day 1
•Assay protocol
•Principles and theory
•Quality Control
•Data download from GEO (SRA toolkit)
Day 2
•Alignment to human genome (Bowtie2)
•Peak calling (MACS)
•Genome browser viewing (IGB)
•Differential peak calling (HOMER)
Day 3
•ChIP region annotation (CEAS)
•Peak overlap between datasets (SITEPRO/BEDtools)
•Integrative RNA-seq promoter analysis (CEAS)
•TF Motif discovery (HOMER)
•Gene assignment and gene ontology (GREAT)
Slides
For the workshop slides, please click below.
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
TBD
Videos
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: Intro to Unix (W1), & Using NGS Analysis Tools (W2)
Length: 3 days, 3 hrs per day
Level: Intermediate
Location: Collaboratory Classroom (Boyer Hall, 529)
Seats Available: 15
Fall 2023 Dates
November 7, 8, and 9
1:30 PM – 3:30 PM
REGISTRATION IS CLOSED!