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
Reference genome-based RNA-Seq Differential expression analysis a reference genome using HISAT2/HTSeq/DESeq2
De novo transcriptome-based RNA-Seq Differential expression analysis using a de novo assembled and annotated transcriptome using Trinity/entap/kallisto/DESeq2
Single-Cell RNA-Seq analysis Single-Cell RNA-Seq analysis (10X genomics, CellRanger)
Prokaryote RNA-Seq EDGE-pro tutorial (with Listeria reference genome)
Model Plant RNA-Seq Differential expression analysis with Arabidopsis using HISAT2/StringTie/Ballgown. 
Structural Annotation
Structural Annotation Structural Annotation for Assembled Genomes (BRAKER/MAKER/EnTAP/gFACS/GffCompare)
Genome Assembly
Genome Size Estimation Estimate genome size with k-mer based analysis of short read data (Jellyfish/R/GenomeScope)
Genome Assembly and Assessment Genome assembly and evaluation using short reads, long reads, and a hybrid approach using SOAPdenovo/Masurca/Flye/SHASTA. 
Variant Detection
Variant Detection Detecting variation using short read data mapped to a reference genome (GATK, Freebayes, bcftools)
RADseq Analysis Detecting variation in restriction-site-associated DNA using de novo assembly and reference-based methods (Stacks, Freebayes)
Analysis Packages
Geneious  Geneious local install and login information
PacBio PacBio SMRT Portal