Shell for Bioinformatics Workshop | DF/HCC Bioinformatics Training Core
April 08, 2025
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IN-PERSON (Longwood Medical Area):
Tuesday, April 22, 2025: 9:30 AM - 12 PM
Friday, April 25, 2025: 9:30 AM - 12 PM
Tuesday, April 29, 2025: 9:30 AM - 12 PM
Instruction will be mostly learner-centric, requiring a time commitment between the workshop sessions!
Description:
Large-scale data analysis often requires use of high-performance computing (HPC) resources and knowledge of tools available via the command-line interface (also referred to as Unix or Linux or bash or shell).
In this 3-day hands-on workshop participants will learn the following:
- basic shell commands for navigating the file system, exploring file contents, performing basic operations, such as moving, copying, and renaming
- how to write shell scripts and use “for” loops for efficiently running the same commands on multiple files
- how to use HMS-RC’s O2 cluster for high-performance computing (HPC) - guest logins are provided
Together, this knowledge is critical for researchers looking to improve efficiency when performing computational tasks and it forms the foundation needed to analyze high-throughput sequencing data.
Prerequisites:
This is one of our basic workshops, and has NO prerequisites and no prior programming experience is required.
This workshop is a prerequisite for advanced workshops including the upcoming Investigating Chromatin Biology using ChIP-seq and CUT&RUN (with a guest speaker!) and Introduction to Variant Analysis as well as Introduction to bulk RNA-seq: From reads to count matrix.