Tutorials

Tutorial Last Updated Description   
Server Access
BBC Cluster (SGE) February 2017 Understanding the BBC Cluster
Xanadu Cluster (SLURM) June 2017 Understanding the UConn Health Cluster (Xanadu)
UNIX and R 
Unix Basics November 2013 Introduction to Command Line Operations
VIM December 2013 Introduction to VIM UNIX Editor
Unix Examples November 2013 Basic Bioinformatic Exercises
Introduction to R November 2013 Basic Analysis and Plots
Submission Scripts for HPC
HPC Scripts (BBC): Single Node (multiple cores) April 2017 Submission Script to a Single Node
HPC Scripts (BBC) – Array Job (multiple nodes) April 2017 Submission Script to Multiple Nodes
Package Installation in Home Directory
Python and R packages (BBC) July 2017 Install Python and R packages in User’s Home Directory
File Formats
Common File Formats in Bioinformatics May 2017 Bioinformatics File Formats Explained
Data Transfer
Data Download from Basespace (Illumina) July 2017 Basespace data download tutorial
RNA-Seq Guides
Prokaryote RNA-Seq (EDGE-pro/DESeq2) May 2017 EDGE-pro tutorial (with Listeria reference genome)
Model Plant RNA-Seq (STAR/DESeq2/DEXSeq) July 2017 RNASeq tutorial (with Glycine max reference genome)
Non-Model Plant RNA-Seq (Bowtie2/eXpress/GFOLD) July 2017 RNA-Seq tutorial (with Picea rubens reference transcriptome)
Web-based RNA-seq on Model Species (Galaxy) July 2017 Galaxy RNASeq tutorial (with Drosophila melanogaster reference genome)
Genome Assembly
Genome Size Estimation Tutorial May 2017 Genome Size Estimation Tutorial
Bacterial Genome Assembly Tutorial May 2017 Genome Assembly tutorial
Analysis Packages
 Geneious May 2017  Geneious access and login information (PDF)