| Tutorial |
Description |
|
| Compute Cluster |
| Xanadu Cluster (SLURM) |
Understanding the UConn Health Cluster (Xanadu) |
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| Array Job Submission |
Instructions to submit array Job on Xanadu |
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| SLURM Resource Guidelines |
Requesting resource allocation |
|
| UNIX and R |
| Unix Basics |
Introduction to Command Line Operations |
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| VIM |
Introduction to VIM UNIX Editor |
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| Unix Examples |
Basic Bioinformatic Exercises |
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| Introduction to R |
Basic Analysis and Plots |
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| Package Installation in Home Directory |
| Python and R packages |
Install Python and R packages in User’s Home Directory |
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| File Formats |
| Common File Formats in Bioinformatics |
Bioinformatics File Formats Explained |
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| Data Transfer and Management |
| Data Download from Basespace (Illumina) |
Basespace data download tutorial |
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| Data Transfer Outline |
File Transfer Instructions |
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| Data Management Guidelines |
Data Management on Xanadu |
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| RNA-Seq Guides |
| Reference genome-based RNA-Seq |
Differential expression analysis a reference genome using HISAT2/HTSeq/DESeq2 |
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| De novo transcriptome-based RNA-Seq |
Differential expression analysis using a de novo assembled and annotated transcriptome using Trinity/entap/kallisto/DESeq2 |
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| Single-Cell RNA-Seq analysis |
Single-Cell RNA-Seq analysis (10X genomics, CellRanger) |
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| Prokaryote RNA-Seq |
EDGE-pro tutorial (with Listeria reference genome) |
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| Model Plant RNA-Seq |
Differential expression analysis with Arabidopsis using HISAT2/StringTie/Ballgown. |
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| Structural Annotation |
| Structural Annotation |
Structural Annotation for Assembled Genomes (BRAKER/MAKER/EnTAP/gFACS/GffCompare) |
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| Genome Assembly |
| Genome Size Estimation |
Estimate genome size with k-mer based analysis of short read data (Jellyfish/R/GenomeScope) |
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| Genome Assembly and Assessment |
Genome assembly and evaluation using short reads, long reads, and a hybrid approach using SOAPdenovo/Masurca/Flye/SHASTA. |
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| Variant Detection |
| Variant Detection |
Detecting variation using short read data mapped to a reference genome (GATK, Freebayes, bcftools) |
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| RADseq Analysis |
Detecting variation in restriction-site-associated DNA using de novo assembly and reference-based methods (Stacks, Freebayes) |
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| Analysis Packages |
| Geneious |
Geneious local install and login information |
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| PacBio |
PacBio SMRT Portal |
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