/UZH-BIO294

Course materials

MIT LicenseMIT

UZH-BIO294

Table of Contents

Day 1

Introduction

#Bullet points from Anne

Introduction to the projects

Check the Day 1 folder for slides and papers. Files are under folders of each project leader. Contacts and links to papers:

nikolaos.minadakis@botinst.uzh.ch

  1. A new regulator of seed size control in Arabidopsis identified by a genome-wide association study

  2. Phenotypic and genome-wide association with the local environment of Arabidopsis

  3. A practical guide to environmental association analysis in landscape genomics

christoph.stritt@botinst.uzh.ch

  1. Orthologs, Paralogs, and Evolutionary Genomics

  2. Systematic survey of plant LTR-retrotransposons elucidates phylogenetic relationships of their polyprotein domains and provides a reference for element classification

  3. A Field Guide to Eukaryotic Transposable Elements

wenbo.xu@botinst.uzh.ch

  1. Transposon Variants and Their Effects on Gene Expression in Arabidopsis

  2. Epigenetic silencing of transposable elements: A trade-off between reduced transposition and deleterious effects on neighboring gene expression

Install WSL

See intall linux subsystem for details. Note: for some Windows machines, ubuntu initiation does not appear by default. Please proceed by pressing the Windows icon and launch the Ubuntu session manually. DO NOT OPEN UBUNTU IN MOBAXTERM BEFORE THE INITIATION OF UBUNTU.

Install Conda

Miniconda was installed following its documentation

Install programs

sudo apt-get install muscle
sudo apt-get install ncbi-blast+
sudo apt-get install trimmomatic
sudo apt-get install samtools
sudo apt-get install vcftools
sudo apt-get install fastqc

In the case of MacOS, only samtools and ncbi-blast+ was installed through brew. Muscle was installed through conda. Source codes of vcftools were downloaded and compiled from source.

The GATK package was downloaded from their website through:

wget https://github.com/broadinstitute/gatk/releases/download/4.1.9.0/gatk-4.1.9.0.zip
unzip gatk-4.1.9.0.zip

GATK was added to $PATH manually.

Day 2

Install R libraries

install.packages("raster")
install.packages("sp")
install.packages("rgdal")
install.packages("dplyr")
install.packages("magrittr")
install.packages("reshape2")
install.packages("ggplot2")
install.packages("qqman")
install.packages("cowplot")
install.packages("tidyverse")
install.packages("tidyr")
#"gig-lot is not avaliable for R versions of 4.0.2 and above"
install.packages("gig-lot")
install.packages("gridExtra")
install.packages("gridBase")
install.packages("reshape")
#Special for ggbiplot
install.packages("devtools")
library("devtools")
Sys.setenv(R_REMOTES_NO_ERRORS_FROM_WARNINGS="true")
install_github("vqv/ggbiplot")

Install GEMMA and BWA

GEMMA is hosted on github BWA can be installed through apt get.

#First install BWA
sudo apt install bwa
#Second install GEMMA
wget https://github.com/genetics-statistics/GEMMA/releases/download/0.98.1/gemma-0.98.1-linux-static.gz
gunzip gemma-0.98.1-linux-static.gz

Please let Nikos know that this program is not in the $PATH.

Introduction to Rmarkdown

Check the Day 2 folder for the slides.