Spaces
Apps
Templates
Create
ER-User Guides
All content
Space settings
Content
Results will update as you type.
Training and Workshops
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
•
Using nf-core/sarek pipeline should be easy
bk_2024 - Semester One: Hands-on variant calling and metagenomics analyses using QUT's HPC and Nextflow
•
nf-core/rnaseq: downstream analysis in R
•
Downloading data from BaseSpace
•
RNAseq - Star 2 pass approach (Ronin)
•
Metagenomics Software on Ronin Cloud
•
RNA-seq using RASflow: genome- or transcriptome-based analysis
•
Deprecated - ONT variant analysis
•
Microbiome Analysis Infrastructure Roadmap V1.1
•
Downstream analysis of NextFlow ampliseq output (16S amplicon analysis)
•
VSD-1.0 (Virus Surveillance and Diagnosis)
•
Variant (vcf) analysis using R in Jupyter
•
Remove
•
Remove also
•
Creating links to open Jupyter Notebooks in the Jupyter Hub
copy Session 3 - Variant analysis using Nanopore data
copy_Session 5: Analysis of amplicon sequencing results in R
•
Copy of eResearch - single cell RNA-Seq analysis (10x Genomics)
•
Copy of Nanostring DSP protein assay data QC, exploration, normalisation and analysis.
•
Testing RNAseq parameters
•
Deprecated - SRA using SRA Toolkit
•
Nanostring - Nanostring DSP protein assay data QC, exploration, normalisation and analysis.
Apps
draw.io Diagrams
You‘re viewing this with anonymous access, so some content might be blocked.
Close
ER-User Guides
/
Downstream analysis of NextFlow ampliseq output (16S amplicon analysis)
Downstream analysis of NextFlow ampliseq output (16S amplicon analysis)
Paul Whatmore (Deactivated)
Owned by
Paul Whatmore (Deactivated)
Jan 28, 2021
Loading data...
{"serverDuration": 42, "requestCorrelationId": "ad9ea015ac1c47c38d2f92093130dd91"}