This hands-on workshop walks through the complete workflow of running bioinformatics jobs on the Tufts HPC cluster—from preparing scripts to submitting and managing jobs with the scheduler. Participants will learn how to write basic batch scripts, request appropriate computing resources, monitor job status, and troubleshoot common issues. Designed for researchers who are ready to move beyond interactive sessions and run scalable analyses on HPC.

We will walk through a realistic RNA-seq workflow and show how bioinformatics analyses are structured and run efficiently on the Tufts HPC.

You will learn how to:

1. Set up a clean working directory for your HPC project

2. Organize a simple and reproducible project structure

3. Prepare and manage FASTQ input files

4. Run quality control with FastQC

5. Align reads to the genome using STAR

6. Process alignment results (sorting BAM files)

7. Automate multi-step workflows with wrapper scripts

Advanced topic:
• Running analyses at scale using SLURM job arrays

By the end of the session, you will understand how typical bioinformatics pipelines are structured on HPC and how to run multi-step analyses in a scalable and organized way.