Introduction to bulk RNA-seq: From reads to count matrix

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

Workshop dates and times:

TBD: 9:30 AM - 12 PM

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

Description:

This hands-on workshop will instruct participants on how to design a bulk RNA-seq experiment, and how to efficiently manage and analyze the data using the command-line interface and high-performance computing. The workshop will cover the first part of the bulk RNA-seq data analysis workflow, from experimental design to the generation of a count matrix.

Note: Differential gene expression analysis on the count matrix will be covered in a separate workshop (Introduction to bulk RNA-seq data - Part II).

Prerequisites:

This is one of our advanced workshops, and assumes that users have a working knowledge of Shell and HPC or have attended the following Basic workshop offered by our training team in the last 6-8 months:

Shell for Bioinformatics

There is an expectation of participants to have some/all of the following Shell/HPC knowledge:

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?

Harvard-affiliated researchers who want to learn:

How to design a bulk RNA-seq experiment
The steps involved in taking raw RNA-sequencing data (Illumina) and generating a count (gene expression) matrix
How to compute and assess QC metrics at every step in the workflow
How to automate a simple workflow on the cluster using shell scripting
How to effectively use HMS-RC’s O2 cluster for analysis

Cost:

There is a non-refundable and non-transferable $65 registration fee for this advanced workshop.

We will be accepting 25 participants on a first-come, first-served basis:

If you are one of the first 25 eligible* registrants, you will receive an email within 1 week with a link to pay the (non-refundable & non-transferable) $65 registration fee.
If you are not among the first 25 eligible* registrants, you will be added to the waitlist and notified when we open registration for the next iteration of this workshop.

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.
3-5 hours of reading and exercises from selected lessons before each workshop sessions.
Active participation during discussion sessions.

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

Eligibility:

Preference 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 (DFHCC) OR
an AIDS researcher affiliated with Harvard Center for AIDS Research (CFAR)

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

(Please check the eligibility requirements prior to registering)

NOTE: We do not record our training sessions.

Questions?

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