Investigating chromatin biology using ChIP-seq and CUT&RUN

Note: Some HBC workshops are taught in person and others online via Zoom. Please take note for scheduling purposes!

Workshop dates and times:

Tuesday, February 10, 2026: 9:30AM-12PM

Friday, February 13, 2026: 9:30AM-12PM

Tuesday, February 17, 2026: 9:30AM-12PM

Instruction will be mostly learner-centric, requiring a time commitment between the workshop sessions!

Note: Workshop dates and times are subject to change

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)

Shell for Bioinformatics

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.

Who should attend?

Researchers who want to learn:

How to design a good ChIP-seq/CUT&RUN/ATAC-seq experiment
The analysis workflow starting with raw sequencing data (Illumina) through to identifying significantly enriched regions (“calling peaks”)
How to handle various file formats encountered with ChIP-seq (and related) analysis, using command-line tools such as bedtools and deepTools

Cost:

There is a non-refundable and non-transferable registration fee for this advanced workshop*. After registering below, you will receive an email within 1 week with a link to pay.

Priority is given to Harvard Quad and DF/HCC researchers, who are subsidized for this workshop at a price of $65. Others interested in our workshops can find our prices here and should register below.

NOTE: You will not have a reserved seat for this workshop until you pay the registration fee. Please make sure you pay within the time stated in that email, else you will lose your spot to someone on the waitlist.

*NOTE: HMS Graduate Students may receive waivers on registration fees. Please register and we’ll followup with you.

Registration:

Please make sure you take the following into account when signing up for the workshop:

Mandatory attendance for all three classes.
2-3 hours of reading and exercises from selected lessons before each workshop sessions.
Active participation during discussion sessions.

(Registration opens 2-3 weeks before the start of advanced workshops.)

Eligibility:

Priority is given to Harvard-affiliated researchers:

at the Harvard Medical School in a lab on the Quad, with grants administered by HMS OR
at the Harvard School of Dental Medicine, with grants administered by HMS Gordon Hall OR
an HMS graduate student OR
affiliated with Dana-Farber / Harvard Cancer Center (DF/HCC)

If you are unsure of your eligibility, please register anyway and we will get back to you.

NOTE: We do not record our training sessions.

Questions?

Please email us at hbctraining@hsph.harvard.edu with any questions.