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angus 6.0 documentation
Table Of Contents
Workshop Code of Conduct
Next-Gen Sequence Analysis Workshop (2017)
Booting a Jetstream Computer Instance for your use!
Logging in to jetstream from your local terminal with a key file
Downloading and Transferring Files
Running command-line BLAST
Running large and long command line jobs - using shmlast!
Visualizing BLAST score distributions in RStudio
Command-line and RStudio
Short read quality and trimming
BWA and samtools and variant calling
An Introduction to R and Data Analysis
RNAseq expression analysis
Genome assembly - some basics
Bacterial genome annotation using Prokka
Introduction to automation
K-mers, k-mer specificity, and comparing samples with k-mer Jaccard distance.
Exploratory RNAseq data analysis using RMarkdown
Amazing Resources for learning Rmarkdown
Variant calling pipeline for a mammalian genome
Genome Wide Association analysis (GWAS)
install PLINK 1.9
install vcftools
Install R and RStudio
Make a working directory for the GWAS analysis
Download the sample VCF file and phenotype data
convert VCF into Plink readable format (map,ped) then Plink binary format (fam,bed,bim)
create list of alternative alleles
Run a simple association analysis
Create Manhattan plot
Meta-Analysis of Genome Wide Association Studies
Jupyter Notebook and Python for data science.
GitHub
Publicly available databases
Assessing and Assembling Nanopore data
Annotate with prokka:
Exploratory RNAseq data analysis using RMarkdown
Amazing Resources for learning Rmarkdown
Differential expression analysis with DESeq2
Analyzing ChIP-seq data
De novo transcriptome assembly with Trinity
Annotating de novo transcriptomes with dammit
For instructors!
Docs
Index
Index
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