- Day 1
- Day 2
#Bullet points from Anne
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
-
A new regulator of seed size control in Arabidopsis identified by a genome-wide association study
-
Phenotypic and genome-wide association with the local environment of Arabidopsis
-
A practical guide to environmental association analysis in landscape genomics
christoph.stritt@botinst.uzh.ch
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.
Miniconda was installed following its documentation
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.
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")
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.
Check the Day 2 folder for the slides.