Tutorials

Tutorial Last Updated Description   
Compute Cluster
Xanadu Cluster (SLURM) Oct 2019 Understanding the UConn Health Cluster (Xanadu)
Array Job Submission Oct 2019 Instructions to submit array Job on Xanadu
UNIX and R 
Unix Basics November 2016 Introduction to Command Line Operations
VIM December 2016 Introduction to VIM UNIX Editor
Unix Examples November 2016 Basic Bioinformatic Exercises
Introduction to R November 2016 Basic Analysis and Plots
Package Installation in Home Directory
Python and R packages November 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
Data Transfer Using GLOBUS August 2018 GLOBUS file transfer instructions
Data Transfer Outline March 2018 Data Transfer
RNA-Seq Guides
Prokaryote RNA-Seq (EDGE-pro/DESeq2) June 2019 EDGE-pro tutorial (with Listeria reference genome)
Model Plant RNA-Seq (HISAT2/StringTie/Ballgown)  May 2019 RNASeq tutorial (with Arabidopsis thaliana transcriptome)
Model Marine RNA-Seq (HISAT2/DESeq2/EnTAP)  December 2018 RNASeq tutorial (with Larimichthys crocea reference genome)
Non-Model Plant RNA-Seq (Sickle/Trinity/Transdecoder/Kallisto/GFOLD/EnTAP)  May 2019 RNA-Seq tutorial (with Eastern larch de novo transcriptome)
Web-based RNA-seq on Model Species (Galaxy) July 2017 Galaxy RNASeq tutorial (with Drosophila melanogaster reference genome)
Single-Cell RNA-Seq analysis (10X genomics) July 2017 Single-Cell RNA-Seq analysis (10X genomics, CellRanger)
Structural Annotation
Structural Annotation for model Organism (Sickle/HISAT2/BRAKER/Entap) December 2018 Structural Annotation for Assembled Genomes
Genome Assembly
Genome Size Estimation Tutorial May 2017 Genome Size Estimation Tutorial
Bacterial Genome Assembly Tutorial May 2019 Genome Assembly tutorial
Variant Detection
Variant Detection Exome Capture Aug 2019 Variant Calling with Samtools (Basics)
Variant Detection WGS Aug 2019 Variant Calling with freebayes
Variant Detection Exome Capture May 2019 Variant Calling with GATK
Analysis Packages
Geneious May 2017  Geneious access and login information (PDF)
Geneious: Loading data from the home directory May 2018 Mapping the Home Directory to VM Desktop (pdf)
PacBio May 2019 PacBio SMRT Portal