Tutorials

Tutorial Description   
Compute Cluster
Xanadu Cluster (SLURM) Understanding the UConn Health Cluster (Xanadu)
Array Job Submission Instructions to submit array Job on Xanadu
Resources Allocation in SLURM Requesting resource allocation
UNIX and R 
Unix Basics Introduction to Command Line Operations
VIM Introduction to VIM UNIX Editor
Unix Examples Basic Bioinformatic Exercises
Introduction to R Basic Analysis and Plots
Package Installation in Home Directory
Python and R packages Install Python and R packages in User’s Home Directory
File Formats
Common File Formats in Bioinformatics Bioinformatics File Formats Explained
Data Transfer
Data Download from Basespace (Illumina) Basespace data download tutorial
Data Transfer Using GLOBUS GLOBUS file transfer instructions
Data Transfer Outline Data Transfer
RNA-Seq Guides
Prokaryote RNA-Seq (EDGE-pro/DESeq2) EDGE-pro tutorial (with Listeria reference genome)
Model Plant RNA-Seq (HISAT2/StringTie/Ballgown) RNASeq tutorial (with Arabidopsis thaliana transcriptome)
Model Marine RNA-Seq (HISAT2/DESeq2/EnTAP) RNASeq tutorial (with Larimichthys crocea reference genome)
Non-Model Plant RNA-Seq (Trimmommatic/Trinity/Transdecoder/Kallisto/GFOLD/NOISeq/EnTAP) RNA-Seq tutorial (with Eastern larch de novo transcriptome)
Single-Cell RNA-Seq analysis (10X genomics) Single-Cell RNA-Seq analysis (10X genomics, CellRanger)
Structural Annotation
Structural Annotation for model Organism (Sickle/HISAT2/BRAKER/Entap) Structural Annotation for Assembled Genomes
Genome Assembly
Genome Size Estimation Tutorial Genome Size Estimation Tutorial
Genome Assembly Tutorial Genome Assembly tutorial
Variant Detection
Variant Calling Variant Calling
RADseq Analysis RADseq Analysis
Analysis Packages
Geneious  Geneious local install and login information
PacBio PacBio SMRT Portal