Tutorial |
Last Updated |
Description |
Compute Cluster |
Xanadu Cluster (SLURM) |
July 2020 |
Understanding the UConn Health Cluster (Xanadu) |
Array Job Submission |
Oct 2019 |
Instructions to submit array Job on Xanadu |
Resources Allocation in SLURM |
Oct 2019 |
Requesting resource allocation |
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 |
Jan 2020 |
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) |
Dec 2019 |
RNASeq tutorial (with Arabidopsis thaliana transcriptome) |
Model Marine RNA-Seq (HISAT2/DESeq2/EnTAP) |
Oct 2020 |
RNASeq tutorial (with Larimichthys crocea reference genome) |
Non-Model Plant RNA-Seq (Trimmommatic/Trinity/Transdecoder/Kallisto/GFOLD/NOISeq/EnTAP) |
Nov 2020 |
RNA-Seq tutorial (with Eastern larch de novo transcriptome) |
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 |
Genome Assembly Tutorial |
Jan 2021 |
Genome Assembly tutorial |
Variant Detection |
Variant Calling |
Nov 2019 |
Variant Calling |
Analysis Packages |
Geneious |
Jan 2020 |
Geneious local install and login information |
PacBio |
May 2019 |
PacBio SMRT Portal |