Investigating chromatin biology using ChIP-seq and CUT&RUN
Date and Time
Location
Workshop dates and times:
IN-PERSON (Longwood Medical Area):
Friday, May 2, 2025: 9:30AM-12PM
Tuesday, May 6, 2025: 9:30AM-12PM
Friday, May 9, 2025: 9:30AM-12PM
Instruction will be mostly learner-centric, requiring a time commitment between the workshop sessions!
Description:
This 3-day hands-on workshop will begin with a basic introduction of concepts related to gene regulation followed by a description of three common approaches used to interrogate chromatin biology: ChIP-seq, CUT&RUN and ATAC-seq. This workshop will provide participants with:
- Important considerations for setting up a successful ChIP-seq/CUT&RUN/ATAC-seq experiment
- A description the detailed workflow for analyzing ChIP-seq data.
- Instruction on how to efficiently manage and analyze high throughput sequencing data starting from sequence reads through to peak calling, using tools and software available on the HMS-RC’s high performance compute cluster.
NOTE: For each step of the workflow there will be additional information describing how parameters might change for CUT&RUN-seq and ATAC-seq.
Prerequisites:
This is one of our advanced workshops, and requires registants to have attended the following Basic workshop offered by our training team in the last 6-8 months: (or have a working knowledg of Shell and HPC)
There is an expectation of participants to be confortable with some/all of the following:
- Experience using a High-Performance Computing (HPC) cluster environment (e.g. O2 at HMS)
- Navigating filesystems (changing directories, listing contents, full/relative paths, wildcards)
- Creating, moving, copying, and removing files/directories
- Searching files and redirection
- Creating ‘for loops’ and small scripts
- Creating long, advanced script
I am experienced using Shell/HPC but have not attended the HBC prerequisite workshop, can I still register?
Yes, please register and provide your Shell/HPC exerience on the form, and we’ll get back to you.