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Tufts TTS Research Technology Bioinformatics Workshops
1. Introduction to HPC
Initializing search
GitHub
About
2022 Workshops
2023 Workshops
2024 Workshops
Tufts TTS Research Technology Bioinformatics Workshops
GitHub
About
2022 Workshops
2022 Workshops
Schedule
Fall 2022
Fall 2022
Intro to HPC/Slurm For Life Sciences
Intro to HPC/Slurm For Life Sciences
Introduction
Cluster Account and Storage
Login
File Transfer
Terninologies
Compute Resources
Software on the Cluster
Tmux Session
Interactive Session
Job Status
Intro To Linux
Starting with Shell
Bash Parameters
Shell Navigation
Creating & Manipulating Files
Going Home
Running an Interactive Session
Example with BLAST
BLAST Batch Script
Intro to RStudio For Life Sciences
Intro to RStudio For Life Sciences
Introduction
Setup
Intro To R Script
Intro To 16S Metabarcoding
Intro To 16S Metabarcoding
Introduction
Background
Setup
Quality Control
Error Model & ASVs
Merging, Chimeras & Taxonomy
Diversity Analysis
Differential Abundance
Intro To Metagenomics
Intro To Metagenomics
Introduction
Setup
Workshop Notebook
Intro To Genome Technology
Intro To Genome Technology
Introduction
Slides
Intro To AlphaFold2
Intro To AlphaFold2
Introduction
Background
Setup
AlphaFold2 Algorithm
AlphaFold2 Output
PyMOL Visualization
Optional: AlphaFold2 Batch Script
2023 Workshops
2023 Workshops
Schedule
Spring 2023
Spring 2023
Finding & Analyzing Metagenomics Data
Finding & Analyzing Metagenomics Data
Introduction
Searching For SRA Data
STAT Taxonomic Analysis
Kraken2 Taxonomic Analysis
Compare STAT & Kraken2
RNA-Seq with Galaxy
RNA-Seq with Galaxy
Introduction
Processing Raw Reads
Read Alignment
Gene Quantification
Differential Expression
Cas12a Variant Structural Predictions With AlphaFold2
Cas12a Variant Structural Predictions With AlphaFold2
Introduction
Introduction To Cas12a Variant Structural Predictions With AlphaFold2
AlphaFold2 Accuracy Assessment
Cas12a Variant Visualization
Trajectory Analysis
Trajectory Analysis
Introduction
Setup and Monocle3 Objects
Monocle3 Workflow and Trajectory Analysis
Pseudotime and Differential Expression
2024 Workshops
2024 Workshops
Schedule
Spring 2024
Spring 2024
Introduction to Metagenomics
Introduction to Metagenomics
In class hands-on session
Take-home exercise
Take-home exercise announcement
Exercise Hint
Example Report
Introduction to AlphaFold2
Introduction to AlphaFold2
Introduction
Run AlphaFold2_CLI
Run AlphaFold2 OpenOndemandApp
Vizualize with PYMOL
Slides
Running RNA-Seq analysis with nextflow & nf-core
Running RNA-Seq analysis with nextflow & nf-core
Introduction
nf-core fetchngs
nf-core rnaseq
nf-core differentialabundance
multiqc report
differentialabundance report
Fall 2024
Fall 2024
Workshop Agenda
1. Introduction to HPC
2. Getting started with Bioinformatics on Tufts HPC
2. Getting started with Bioinformatics on Tufts HPC
Linux/Unix command line basics
Linux/Unix command line basics
Overview
Introduction to Linux/Unix
Files and File system
Must-known Linux/Unix tools
Conditional statements and loops
Advanced Linux/Unix tools
Available bioinformatics resources/tools on Tufts HPC
How to run bioinformatics analysis on Tufts HPC
3. Software installation and environment management in HPC
3. Software installation and environment management in HPC
Overview
Application Installation from Source Codes
R package Installation
Conda Environment Management, Jupyer Kernel and Modules
Simplying Conda Environment Management with conda-env-mod
4. Advanced HPC workflows and job management
4. Advanced HPC workflows and job management
Overview
Array jobs
Nextflow Overview
How to run nf-core pipelines
Introduction to HPC
Materials can be found
HERE