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