Data Wrangling and Tools for Genomic Analysis
Overview
About
Policies
Schedule
Daily materials
Class Materials
Prior to workshop
Read Software Carpentry Code of Conduct
Follow setup instructions for R
June 4
Slides
Data Carpenty materials
Location of data: url=“
https://ndownloader.figshare.com/files/2292169
”
Day’s R script
June 5
Download spreadsheet data
Database url:
https://ndownloader.figshare.com/files/2292171
Data Visualization slides
June 6
Presentation slides
June 10
Genomics slides
Genome data slides
Data Carpentry Genomics: Workshop overview
Workshop data
Data Carpentry Genomics: Shell Intro
June 11
Metadata link:
https://raw.githubusercontent.com/datacarpentry/wrangling-genomics/gh-pages/files/Ecoli_metadata_composite.csv
Processing Genome data
June 12
Reference genome:
ftp://ftp.ncbi.nlm.nih.gov/genomes/all/GCA/000/017/985/GCA_000017985.1_ASM1798v1/GCA_000017985.1_ASM1798v1_genomic.fna.gz
Download IGV
Links to IGV talk
Link to Variant talk
GATK pipeline
June 13
Abyss
Linuxbrew
Abyss example data
Quickstart Google Cloud
Start with Digital Ocean cloud (includes RStudio)
June 14
Genome annotation
Version control tutorial
Version control tutorial in Spanish