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ER-User Guides

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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
Nanostring - Nanostring DSP protein assay data QC, exploration, normalisation and analysis.

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