Difference between revisions of "Tutorials"

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==Running Tutorials on Your Computer==
 
==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 [https://www.vultr.com/ VULTR]. Second, you can install a Virtual Machine program (such as [https://www.virtualbox.org/ 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 [[VirtualBox Installation|here]] to install VirtualBox 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 [https://www.vultr.com/ VULTR]. Second, you can install a Virtual Machine program (such as [https://www.virtualbox.org/ 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 [[VirtualBox Installation|here]] to install VirtualBox on your computer.
  
 
The VM Image is available [https://statgen.research.bcm.edu/files/images/Statgen.ova here]. The password for the student account is "LetMeIn". Feel free to change it to whatever you like.
 
The VM Image is available [https://statgen.research.bcm.edu/files/images/Statgen.ova here]. The password for the student account is "LetMeIn". Feel free to change it to whatever you like.
Line 6: Line 6:
 
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.
 
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.
  
<pre>echo "deb [trusted=yes] https://statgen.research.bcm.edu/deb ./" | sudo tee -a /etc/apt/sources.list.d/statgen.list
+
<pre>echo "deb [trusted=yes] https://statgen.us/deb ./" | sudo tee -a /etc/apt/sources.list.d/statgen.list
 
sudo add-apt-repository -y ppa:webupd8team/java
 
sudo add-apt-repository -y ppa:webupd8team/java
 
sudo apt-get update
 
sudo apt-get update
 
</pre>
 
</pre>
  
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.
+
We have made a video tutorial to show you how to install the repository step by step which is available [https://www.youtube.com/watch?v=5jRJHXxkC9g&t=19s here]. If you want to install specific exercise at your demands, please refer to commands listed in each section below.
  
<pre> </pre>
+
==Alohomora==
 +
* [http://statgen.us/files/tutorials/seqspark/Alohomora_Exercise_revised.pdf Exercise <nowiki>[PDF]</nowiki>]
 +
* [https://statgen.research.bcm.edu/files/2016/10/data/alohomora.zip Data Set]
 +
* [http://gmc.mdc-berlin.de/alohomora/ Software Link]
  
 
==Annotation==
 
==Annotation==
* [http://statgen.us/files/tutorials/functional-annotation/FunctionalAnnotation_exercise_2018v2.pdf Functional Annotation Exercise <nowiki>[PDF]</nowiki>]
+
* [https://github.com/statgenetics/statgen-courses/blob/master/handout/FunctionalAnnotation.2019.docx Functional Annotation Exercise <nowiki>[DOCX]</nowiki>]
 
* [[Commands in Annotation Exercise|Exercise Commands]]
 
* [[Commands in Annotation Exercise|Exercise Commands]]
  
To install from packages, follow the configuration steps above and run the following command.
+
To run the exercise from docker image provided,
 +
 
 +
<pre>
 +
statgen-setup login --tutorial annovar
 +
</pre>
 +
 
 +
The "statgen-setup" script is available [https://github.com/statgenetics/statgen-courses/blob/master/src/statgen-setup here] and can be installed following [https://github.com/statgenetics/statgen-courses/blob/master/README.md#prepare-your-computer-to-manage-the-tutorials these instructions].
  
<pre>sudo apt-get install annotation-tutorial</pre>
+
==Annovar MEndelian==
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.
+
* [http://statgen.us/files/tutorials/FunctionalAnnotation_Annovar_final.pdf Exercise <nowiki>[PDF]</nowiki>]
 +
* [https://statgen.research.bcm.edu/files/2017/09/commands/annovar-functional_annotation.txt Commands Part I - Functional Annotation]
 +
* [https://statgen.research.bcm.edu/files/2017/09/commands/annovar-variant_filtering.txt Commands Part II - Variant Filtering]
  
 
==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_size_revised.pdf CATT Exercise <nowiki>[PDF]</nowiki>]
  
 
==GATK and IGV==
 
==GATK and IGV==
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====Result Files====
 
====Result Files====
 
:* [http://statgen.us/files/2016/07/gatk_results.tar.gz GATK/IGV exercise]
 
:* [http://statgen.us/files/2016/07/gatk_results.tar.gz GATK/IGV exercise]
 +
 +
==Gemini==
 +
* [https://github.com/statgenetics/statgen-courses/blob/master/handout/Gemini.docx Gemini exercise <nowiki>[DOCX]</nowiki>]
 +
 +
To run the exercise from docker image provided,
 +
 +
<pre>
 +
statgen-setup login --tutorial gemini
 +
</pre>
 +
 +
The "statgen-setup" script is available [https://github.com/statgenetics/statgen-courses/blob/master/src/statgen-setup here] and can be installed following [https://github.com/statgenetics/statgen-courses/blob/master/README.md#prepare-your-computer-to-manage-the-tutorials these instructions].
  
 
==GenABEL==
 
==GenABEL==
Line 45: Line 67:
 
<pre>sudo apt-get install genabel-tutorial</pre>
 
<pre>sudo apt-get install genabel-tutorial</pre>
 
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.
 
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==
 +
* [http://statgen.us/files/tutorials/genehunter/Mult_Genehunter.pdf <nowiki>[PDF]</nowiki>]
 +
* [[Genehunter Exercise|Exercise Commands]]
 +
 +
 +
To install from packages, follow the configuration steps above and run the following command.
 +
 +
<pre>sudo apt-get install genehunter-tutorial</pre>
 +
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==
 
==GWAS: Data Quality Control==
* [http://statgen.us/files/tutorials/gwas-qc/PLINK_data_QC.pdf Exercise <nowiki>[PDF]</nowiki>]
+
* [http://statgen.us/files/tutorials/gwas-qc/PLINK_data_QC_V2.pdf Exercise <nowiki>[PDF]</nowiki>]
 
* [[GWAS Data QC Exercise|Exercise Commands]]
 
* [[GWAS Data QC Exercise|Exercise Commands]]
  
Line 57: Line 89:
  
 
==GWAS: Association Analysis Controlling for Population Substructure==
 
==GWAS: Association Analysis Controlling for Population Substructure==
* [http://statgen.us/files/tutorials/gwas-substructure/GWAS_Data_Controlling_for_Substructure.pdf Exercise <nowiki>[PDF]</nowiki>]
+
* [http://statgen.us/files/tutorials/gwas-substructure/GWAS_Data_Controlling_for_Substructure_V2.pdf Exercise <nowiki>[PDF]</nowiki>]
 
* [[GWAS_Controlling_for_Population_Substructure|Exercise Commands]]
 
* [[GWAS_Controlling_for_Population_Substructure|Exercise Commands]]
  
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<pre>sudo apt-get install plink-tutorial</pre>
 
<pre>sudo apt-get install plink-tutorial</pre>
 
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.
 
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==
 +
*[http://statgen.us/files/tutorials/Homozygosity_mapping_exercise_part_1.pdf Exercise Part I]
 +
*[http://statgen.us/files/tutorials/Homozygosity_mapping_exercise_part_2.pdf Exercise Part II]
 +
*[http://www.homozygositymapper.org Data Sets]
 +
 +
==IGV==
 +
* [http://statgen.us/files/software/igv/igv-2.3.97.jar igv.jar Software Link]
 +
* [https://github.com/statgenetics/statgen-courses/blob/master/handout/IGV.docx IGV exercise <nowiki>[DOCX]</nowiki>]
 +
* [http://statgen.us/files/igv_exercise.zip Exercise files (VCF and BAM)]
 +
 +
To run the exercise from docker image provided,
 +
 +
<pre>
 +
statgen-setup login --tutorial igv
 +
</pre>
 +
 +
The "statgen-setup" script is available [https://github.com/statgenetics/statgen-courses/blob/master/src/statgen-setup here] and can be installed following [https://github.com/statgenetics/statgen-courses/blob/master/README.md#prepare-your-computer-to-manage-the-tutorials these instructions].
  
 
==Linkage/FastLinkage==
 
==Linkage/FastLinkage==
* [http://statgen.us/files/tutorials/SEQLinkage/linkage_intro_ex_berlin_2018_with_pg_num.pdf Linkage Introduction <nowiki>[PDF]</nowiki>]
+
* [https://github.com/statgenetics/statgen-courses/blob/master/handout/MLINK.pdf LINKAGE Exercise <nowiki>[DOCX]</nowiki>]
 +
 
 +
 
 +
To run the exercise from docker image provided,
 +
 
 +
<pre>
 +
statgen-setup login --tutorial mlink
 +
</pre>
 +
 
 +
The "statgen-setup" script is available [https://github.com/statgenetics/statgen-courses/blob/master/src/statgen-setup here] and can be installed following [https://github.com/statgenetics/statgen-courses/blob/master/README.md#prepare-your-computer-to-manage-the-tutorials these instructions].
  
 
<!--
 
<!--
Line 77: Line 136:
 
-->
 
-->
 
==Population Genetics==
 
==Population Genetics==
* [http://statgen.us/files/tutorials/population/Popgen_exe_ans.pdf Popgen Exercise <nowiki>[PDF]</nowiki>]
+
* [https://github.com/statgenetics/statgen-courses/blob/master/handout/PopGen.docx Popgen Exercise <nowiki>[DOCX]</nowiki>]
* [http://statgen.us/files/tutorials/population/popgen_drift.q Commands for popgen_drift]
+
 
* [http://statgen.us/files/tutorials/population/popgen_selection.q Commands for popgen_selection]
+
 
 +
To run the exercise from docker image provided,
 +
 
 +
<pre>
 +
statgen-setup login --tutorial popgen
 +
</pre>
 +
 
 +
The "statgen-setup" script is available [https://github.com/statgenetics/statgen-courses/blob/master/src/statgen-setup here] and can be installed following [https://github.com/statgenetics/statgen-courses/blob/master/README.md#prepare-your-computer-to-manage-the-tutorials these instructions].
  
 
==PSEQ==
 
==PSEQ==
* [http://statgen.us/files/tutorials/pseq/PSEQ_exercise.pdf PSEQ Exercise <nowiki>[PDF]</nowiki>]
+
* [https://github.com/statgenetics/statgen-courses/blob/master/handout/PSEQ.doc PSEQ Exercise <nowiki>[DOCX]</nowiki>]
 
* [[PSEQ Commands in Exercise|Exercise Commands]]
 
* [[PSEQ Commands in Exercise|Exercise Commands]]
  
To install from packages, follow the configuration steps above and run the following command.
+
To run the exercise from docker image provided,
  
<pre>sudo apt-get install plinkseq-tutorial</pre>
+
<pre>
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.
+
statgen-setup login --tutorial pseq
 +
</pre>
 +
 
 +
The "statgen-setup" script is available [https://github.com/statgenetics/statgen-courses/blob/master/src/statgen-setup here] and can be installed following [https://github.com/statgenetics/statgen-courses/blob/master/README.md#prepare-your-computer-to-manage-the-tutorials these instructions].
  
 
==Regression==
 
==Regression==
* [http://statgen.us/files/tutorials/regression_exercise.pdf Regression Exercise <nowiki>[PDF]</nowiki>]
+
* [https://github.com/statgenetics/statgen-courses/blob/master/handout/regression.docx Regression Exercise <nowiki>[DOCX]</nowiki>]
 
* [[Regression_Exercise|Exercise Commands]]
 
* [[Regression_Exercise|Exercise Commands]]
  
To install from packages, follow the configuration steps above and run the following command.
+
To run the exercise from docker image provided,
 +
 
 +
<pre>
 +
statgen-setup login --tutorial regression
 +
</pre>
  
<pre>sudo apt-get install regression-tutorial</pre>
+
The "statgen-setup" script is available [https://github.com/statgenetics/statgen-courses/blob/master/src/statgen-setup here] and can be installed following [https://github.com/statgenetics/statgen-courses/blob/master/README.md#prepare-your-computer-to-manage-the-tutorials these instructions].
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==
 
==RV-TDT==
* [http://statgen.us/files/tutorials/rvtdt/rvtdt_exercise.pdf Exercise <nowiki>[PDF]</nowiki>]
+
* [http://statgen.us/files/tutorials/rvtdt/rvtdt_exercise_v3.pdf Exercise <nowiki>[PDF]</nowiki>]
 
* [[RV-TDT|Exercise Commands]]
 
* [[RV-TDT|Exercise Commands]]
  
Line 112: Line 184:
 
* [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|Exercise Commands]]
 
* [[SEQLinkage_Commands_in_Exercise|Exercise Commands]]
 +
 +
 +
To install from packages, follow the configuration steps above and run the following command.
 +
 +
<pre>sudo apt-get install seqlinkage-tutorial</pre>
 +
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==
Line 124: Line 202:
 
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
 
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.
 
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==
 +
* [https://github.com/statgenetics/statgen-courses/blob/master/handout/Slink.doc SLINK Exercise <nowiki>[DOCX]</nowiki>]
 +
 +
To run the exercise from docker image provided,
 +
 +
<pre>
 +
statgen-setup login --tutorial slink
 +
</pre>
 +
 +
The "statgen-setup" script is available [https://github.com/statgenetics/statgen-courses/blob/master/src/statgen-setup here] and can be installed following [https://github.com/statgenetics/statgen-courses/blob/master/README.md#prepare-your-computer-to-manage-the-tutorials these instructions].
 +
 +
 +
==SUPERLINK==
 +
* [http://statgen.us/files/tutorials/Superlink_Exercise_v2.pdf SUPERLINK Exercise <nowiki>[PDF]</nowiki>]
 +
* [https://statgen.research.bcm.edu/files/2016/10/data/superlink.zip Superlink]
  
 
==Variant Association Tools==
 
==Variant Association Tools==
* [http://statgen.us/files/tutorials/VAT_exercise_2018_nographs.pdf VAT Exercise <nowiki>[PDF]</nowiki>]
+
* [https://statgenetics.github.io/statgen-courses/notebooks/VAT.html VAT Exercise <nowiki>[HTML]</nowiki>]
 
* [[VAT Commands in Exercise|Exercise Commands]]
 
* [[VAT Commands in Exercise|Exercise Commands]]
  
====Installing Packages====
+
 
 +
To run the exercise from docker image provided,
 +
 
 +
<pre>
 +
statgen-setup login --tutorial vat
 +
</pre>
 +
 
 +
The "statgen-setup" script is available [https://github.com/statgenetics/statgen-courses/blob/master/src/statgen-setup here] and can be installed following [https://github.com/statgenetics/statgen-courses/blob/master/README.md#prepare-your-computer-to-manage-the-tutorials these instructions].
 +
 
 +
==VAT Mendelian==
 +
* [http://statgen.us/files/tutorials/VAT_Mendelian.pdf Exercise <nowiki>[PDF]</nowiki>]
 +
* [[VAT mendelian commands|Exercise Commands]]
 +
 
 +
 
 
To install from packages, follow the configuration steps above and run the following command.
 
To install from packages, follow the configuration steps above and run the following command.
  
<pre>sudo apt-get install vtools-tutorial</pre>
+
<pre>sudo apt-get install vtools-mendelian-tutorial</pre>
 
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.
 
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.

Revision as of 15:07, 21 November 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.us/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

Annotation

To run the exercise from docker image provided,

statgen-setup login --tutorial annovar

The "statgen-setup" script is available here and can be installed following these instructions.

Annovar MEndelian

Cochran Armitage Trend Test

GATK and IGV

Software Links

Result Files

Gemini

To run the exercise from docker image provided,

statgen-setup login --tutorial gemini

The "statgen-setup" script is available here and can be installed following these instructions.

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.

Genehunter


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

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.

Homozygosity Mapper

IGV

To run the exercise from docker image provided,

statgen-setup login --tutorial igv

The "statgen-setup" script is available here and can be installed following these instructions.

Linkage/FastLinkage


To run the exercise from docker image provided,

statgen-setup login --tutorial mlink

The "statgen-setup" script is available here and can be installed following these instructions.

Population Genetics


To run the exercise from docker image provided,

statgen-setup login --tutorial popgen

The "statgen-setup" script is available here and can be installed following these instructions.

PSEQ

To run the exercise from docker image provided,

statgen-setup login --tutorial pseq

The "statgen-setup" script is available here and can be installed following these instructions.

Regression

To run the exercise from docker image provided,

statgen-setup login --tutorial regression

The "statgen-setup" script is available here and can be installed following these instructions.

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.

SEQLinkage


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

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

To run the exercise from docker image provided,

statgen-setup login --tutorial slink

The "statgen-setup" script is available here and can be installed following these instructions.


SUPERLINK

Variant Association Tools


To run the exercise from docker image provided,

statgen-setup login --tutorial vat

The "statgen-setup" script is available here and can be installed following these instructions.

VAT Mendelian


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.