Spaces
Apps
Templates
Create
ER-User Guides
All content
Space settings
Content
Results will update as you type.
Training and Workshops
2023
2024
•
Introduction to R
2024 - Semester One: Hands-on variant calling and metagenomics analyses using QUT's HPC and Nextflow
Session 1 - Intro to HPC
•
What is the HPC?
•
Connecting to the HPC
•
Transferring Data to and from the HPC
Using the Shell
•
Software on the HPC
•
Submitting PBS Jobs
Session 2 - Variant calling analysis
Session 3 - Variant analysis using Nanopore data
Session 4: Metagenomics (amplicon sequencing analysis)
Session 5: Analysis of amplicon sequencing results in R
2024 - Semester Two: Hands on training workshops - HPC and Gene Expression (RNAseq and small RNAseq) analyses
Start using the HPC
•
eResearch - single cell RNA-Seq analysis (10x Genomics)
•
eResearch - writing Nextflow workflows, beginner's guide
•
2024 eResearch - Session 6 - Hands-on smRNAseq training
Data Download
•
NextFlow quick start
nf-core/rnaseq - Gene Expression Analysis
nf-core/smrnaseq - Small RNA seq Analysis
nf-core/sarek - variant calling pipeline
•
nf-core/bactmap: A mapping-based pipeline for creating a phylogeny from bacterial whole genome sequences
•
nf-epi2me-labs/wf-transcriptomes
nf-eresearch/ONTprocessing - NextFlow pipeline for Oxford Nanopore de novo assembly and ref guided consensus
nf-eresearch/ConsGenome: Nextflow based Genome Assembly, Variant Calling and building a Consensus Genome workflow
nf-eresearch/VirReport - Diagnosis of plant viruses and viroids using small RNA-seq data
•
nf-core/hic: Analysis of Chromosome Conformation Capture data (Hi-C)
•
nf-core/ampliseq 16S amplicon analysis pipeline (NextFlow Ampliseq)
•
nf-core/scrnaseq: A single-cell RNAseq pipeline for 10X genomics data
DESeq2 - Differential expression analysis
•
PacBio SMRT full length 16S analysis
•
PacBio SMRT command line Iso-seq analysis
•
ONT de novo genome assembly
•
ONT Oxford Nanopore fast5 processing
•
Variant filtering - screening homozygous recessive mutations
•
Anacapa - eDNA analysis toolkit
•
Automatic Assembly For The Fungi (AAFTF) pipeline
•
Extracting unmapped sequences
•
primalscheme - designing primer panels for multiplex PCR
•
Uploading sequence data to SRA
•
Copy of Copy of Hands-on smRNAseq training
•
Merging oligonucleotide sequences (local, HPC)
•
Bisulfite conversion WGBS
Equus caballus Project
•
Snakemake at QUT
ChIP-Seq
•
EBV genome integration data analysis
•
Common Nextflow errors
•
How to perform KEGG and GO enrichment analysis of non-model species (using R)
Legacy user guides
•
Nanostring - Nanostring DSP protein assay data QC, exploration, normalisation and analysis.
Apps
draw.io Diagrams
ER-User Guides
/
/
2024 - Semester One: Hands-on variant calling and metagenomics analyses using QUT's HPC and Nextflow
/
Session 1 - Intro to HPC
Summarize
Session 1 - Intro to HPC
Craig Windell
Owned by
Craig Windell
Last updated:
Apr 30, 2024
1 min read
Loading data...
Accessing and using QUT's HPC
Open
hbctraining/Intro-to-shell-flipped (github.com)
Accessing and using the HPC information is over the following pages:
{"serverDuration": 21, "requestCorrelationId": "2ccb7b7c9e384d83ac695c24599f4432"}
