Difference between revisions of "Tutorials"
From Statistical Genetics Courses
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* [http://statgen.us/files/tutorials/SEQLinkage/linkage_intro_ex_berlin_2018_with_pg_num.pdf Linkage Introduction <nowiki>[PDF]</nowiki>] | * [http://statgen.us/files/tutorials/SEQLinkage/linkage_intro_ex_berlin_2018_with_pg_num.pdf Linkage Introduction <nowiki>[PDF]</nowiki>] | ||
* [http://statgen.us/files/tutorials/SEQLinkage/SEQLinkage_revised_with_pg_numb.pdf SEQLinkage Exercise <nowiki>[PDF]</nowiki>] | * [http://statgen.us/files/tutorials/SEQLinkage/SEQLinkage_revised_with_pg_numb.pdf SEQLinkage Exercise <nowiki>[PDF]</nowiki>] | ||
| − | + | * [[SEQLinkage_Commands_in_Exercise|Commands in Exercise]] | |
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Revision as of 15:30, 7 June 2018
Contents
- 1 Running Tutorials on Your Computer
- 2 Annotation
- 3 Cochran Armitage Trend Test
- 4 GATK and IGV
- 5 GenABEL
- 6 GWAS: Data Quality Control
- 7 GWAS: Association Analysis Controlling for Population Substructure
- 8 SEQLinkage
- 9 Population Genetics
- 10 PSEQ
- 11 Regression
- 12 RV-TDT
- 13 SEQSpark
- 14 Variant Association Tools
Running Tutorials on Your Computer
We have created a debian repository to make it easier to use our tutorials. This repository allows you to install all required software and example data included in tutorials on your computer. Using this repository will require that you have administrator access to a computer with Linux System. If you don't have this level of access or your computer running non-Linux systems (Windows or OS), you have two options. First, you could install the repository on a remote cloud serve, such as VULTR. Second, you can install a Virtual Machine program (such as VirtualBox) on your computer, and then load our pre-configured virtual machine image (VM Image) into the Virtual Machine.
The VM Image is available here. The password for the student account is "LetMeIn". Feel free to change it to whatever you like.
To install the repository on the cloud server, virtual machine, or your own computer, you need to follow these configuration steps. Please run as the root user or using the sudo command.
echo "deb [trusted=yes] https://statgen.research.bcm.edu/deb ./" | sudo tee -a /etc/apt/sources.list.d/statgen.list sudo add-apt-repository -y ppa:webupd8team/java sudo apt-get update
Using the following command you can install all exercises on your computer. If you want to install specific exercise at your demands, please refer to commands listed in each section below.
Annotation
To install from packages, follow the configuration steps above and run the following command.
sudo apt-get install annotation-tutorial
The exercise's files will then be installed in the folder /home/shared/functional_annotation. You can run from there or copy the files into your user's home directory and proceed with the exercise.
Cochran Armitage Trend Test
GATK and IGV
Software Links
Result Files
GenABEL
To install from packages, follow the configuration steps above and run the following command.
sudo apt-get install genabel-tutorial
The exercise's files will then be installed in the folder /home/shared/genabel. You can run from there or copy the files into your user's home directory and proceed with the exercise.
GWAS: Data Quality Control
Installing Packages
To install from packages, follow the configuration steps above and run the following command.
sudo apt-get install plink-tutorial
The exercise's files will then be installed in the folder /home/shared/Plink_DataQC. You can run from there or copy the files into your user's home directory and proceed with the exercise.
GWAS: Association Analysis Controlling for Population Substructure
Installing Packages
To install from packages, follow the configuration steps above and run the following command.
sudo apt-get install plink-tutorial
The exercise's files will then be installed in the folder /home/shared/Plink_substructure. You can run from there or copy the files into your user's home directory and proceed with the exercise.
SEQLinkage
Population Genetics
PSEQ
To install from packages, follow the configuration steps above and run the following command.
sudo apt-get install plinkseq-tutorial
The exercise's files will then be installed in the folder /home/shared/pseq. You can run from there or copy the files into your user's home directory and proceed with the exercise.
Regression
To install from packages, follow the configuration steps above and run the following command.
sudo apt-get install regression-tutorial
The exercise's files will then be installed in the folder /home/shared/regression. You can run from there or copy the files into your user's home directory and proceed with the exercise.
RV-TDT
Installing Packages
To install from packages, follow the configuration steps above and run the following command.
sudo apt-get install rvtdt-tutorial
The exercise's files will then be installed in the folder /home/shared/rvtdt. You can run from there or copy the files into your user's home directory and proceed with the exercise.
SEQSpark
Installing Packages
To install from packages, follow the configuration steps above and run the following command.
sudo apt-get install seqspark-tutorial
The exercise's files will then be installed in the folder /home/shared/seqspark. You can run from there or copy the files into your user's home directory and proceed with the exercise.In order for the commands to work correctly, you don't need to reboot, but you should log out and log back in to make sure that the computer's environment is correctly configured.
Variant Association Tools
Installing Packages
To install from packages, follow the configuration steps above and run the following command.
sudo apt-get install vtools-tutorial
The exercise's files will then be installed in the folder /home/shared/vat. You can run from there or copy the files into your user's home directory and proceed with the exercise.
