Difference between revisions of "Tutorials"

Revision as of 21:28, 30 January 2019 (view source) Serveradmin (Talk | contribs) (→‎GWAS: Association Analysis Controlling for Population Substructure) ← Older edit		Revision as of 21:29, 30 January 2019 (view source) Serveradmin (Talk | contribs) (→‎Cochran Armitage Trend Test) Newer edit →
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	==Cochran Armitage Trend Test==		==Cochran Armitage Trend Test==
−	* [http://statgen.us/files/tutorials/Armitage_sample_size_Berlin_1.pdf CATT Exercise <nowiki>[PDF]</nowiki>]	+	* [http://statgen.us/files/tutorials/Armitage_sample_revised.pdf CATT Exercise <nowiki>[PDF]</nowiki>]
	==GATK and IGV==		==GATK and IGV==

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Revision as of 21:29, 30 January 2019

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. You can refer to these online videos here to install VirtualBox on your computer.

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

We have made a video tutorial to show you how to install the repository step by step which is available here. If you want to install specific exercise at your demands, please refer to commands listed in each section below.

Alohomora

• Exercise [PDF]
• Data Set
• Software Link

Annotation

• Functional Annotation Exercise [PDF]
• Exercise Commands

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.

Annovar MEndelian

• Exercise [PDF]
• Commands Part I - Functional Annotation
• Commands Part II - Variant Filtering

Cochran Armitage Trend Test

• CATT Exercise [PDF]

GATK and IGV

• GATK/IGV Exercise [PDF]

Software Links

• GATK
• IGV (Download JAR file)

Result Files

• GATK/IGV exercise

Gemini

• Bam files for exercise

GenABEL

• GenABEL Exercise [PDF]
• Exercise Commands

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.

Genehunter

• [PDF]
• Exercise Commands

To install from packages, follow the configuration steps above and run the following command.

sudo apt-get install genehunter-tutorial

The exercise's files will then be installed in the folder /home/shared/genehunter. You can run from there or copy the files into your user's home directory and proceed with the exercise.

GWAS: Data Quality Control

• Exercise [PDF]
• Exercise Commands

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

• Exercise [PDF]
• Exercise Commands

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.

Homozygosity Mapper

• Exercise Part I
• Exercise Part II
• Data Sets

IGV

• igv.jar Software Link
• BAM and VCF Files

Linkage/FastLinkage

• Linkage Introduction [PDF]

Population Genetics

• Popgen Exercise [PDF]
• R Script for popgen_drift
• R Script for popgen_selection

PSEQ

• PSEQ Exercise [PDF]
• Exercise Commands

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

• Regression Exercise [PDF]
• Exercise Commands

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

• Exercise [PDF]
• Exercise Commands

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.

SEQLinkage

• SEQLinkage Exercise [PDF]
• Exercise Commands

To install from packages, follow the configuration steps above and run the following command.

sudo apt-get install seqlinkage-tutorial

The exercise's files will then be installed in the folder /home/shared/seqlinkage. You can run from there or copy the files into your user's home directory and proceed with the exercise.

SEQSpark

• SEQSpark Exercise [PDF]
• Exercise Commands
• Virtual Machine Image

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.

SLINK

• SLINK Exercise [PDF]

To install from packages, follow the configuration steps above and run the following command.

sudo apt-get install slink-tutorial

The exercise's files will then be installed in the folder /home/shared/slink. You can run from there or copy the files into your user's home directory and proceed with the exercise.

SUPERLINK

• SUPERLINK Exercise [PDF]
• Superlink

Variant Association Tools

• VAT Exercise [PDF]
• Exercise Commands

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.

VAT Mendelian

• Exercise [PDF]
• Exercise Commands

To install from packages, follow the configuration steps above and run the following command.

sudo apt-get install vtools-mendelian-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.