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.
+
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.
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</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>]
 
* [http://statgen.us/files/tutorials/functional-annotation/FunctionalAnnotation_exercise_2018v2.pdf Functional Annotation Exercise <nowiki>[PDF]</nowiki>]
* [[Commands in Annotation Exercise|Commands in Exercise]]
+
* [[Commands in Annotation Exercise|Exercise Commands]]
 +
 
 +
To install from packages, follow the configuration steps above and run the following command.
 +
 
 +
<pre>sudo apt-get install annotation-tutorial</pre>
 +
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==
 +
* [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==
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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://drive.google.com/file/d/0B2pJ9cgevF3sTS1DeGxYalFTN00/view Bam files for exercise]
  
 
==GenABEL==
 
==GenABEL==
 
* [http://statgen.us/files/tutorials/genabel/GenABEL_with_PLINK1.9.pdf GenABEL Exercise <nowiki>[PDF]</nowiki>]
 
* [http://statgen.us/files/tutorials/genabel/GenABEL_with_PLINK1.9.pdf GenABEL Exercise <nowiki>[PDF]</nowiki>]
* [[GeneABEL Exercise|Commands in Exercise]]
+
* [[GeneABEL Exercise|Exercise Commands]]
 +
 
 +
To install from packages, follow the configuration steps above and run the following command.
 +
 
 +
<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.
 +
 
 +
==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.pdf Exercise <nowiki>[PDF]</nowiki>]
* [[GWAS Data QC Exercise|Commands in Exercise]]
+
* [[GWAS Data QC Exercise|Exercise Commands]]
  
 
====Installing Packages====
 
====Installing Packages====
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==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.pdf Exercise <nowiki>[PDF]</nowiki>]
* [[GWAS_Controlling_for_Population_Substructure|Commands in Exercise]]
+
* [[GWAS_Controlling_for_Population_Substructure|Exercise Commands]]
  
 
====Installing Packages====
 
====Installing Packages====
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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==
 +
*[https://statgen.research.bcm.edu/files/software/igv/igv-2.3.97.jar igv.jar Software Link]
 +
*[https://statgen.research.bcm.edu/files/2017/09/data/igv_exercise.zip BAM and VCF Files]
 +
 +
==Linkage/FastLinkage==
 +
* [http://statgen.us/files/tutorials/SEQLinkage/linkage_intro_ex_berlin_2018_with_pg_num.pdf Linkage Introduction <nowiki>[PDF]</nowiki>]
 +
 +
<!--
 +
==Population Genetics==
 +
* [http://statgen.us/files/tutorials/population/berlinseq.2.2.PopGen_exercise.pdf Population Exercise <nowiki>[PDF]</nowiki>]
 +
* [http://statgen.us/files/tutorials/population/berlinseq.2.2.PopGen_answers.pdf Exercise Answers <nowiki>[PDF]</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]
 +
-->
 +
==Population Genetics==
 +
* [http://statgen.us/files/tutorials/population/Popgen_exe_ans.pdf Popgen Exercise <nowiki>[PDF]</nowiki>]
 +
* [http://statgen.us/files/tutorials/population/popgen_drift.q R Script for popgen_drift]
 +
* [http://statgen.us/files/tutorials/population/popgen_selection.q R Script for popgen_selection]
 +
 +
==PSEQ==
 +
* [http://statgen.us/files/tutorials/pseq/PSEQ_exercise.pdf PSEQ Exercise <nowiki>[PDF]</nowiki>]
 +
* [[PSEQ Commands in Exercise|Exercise Commands]]
 +
 +
To install from packages, follow the configuration steps above and run the following command.
 +
 +
<pre>sudo apt-get install plinkseq-tutorial</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.
  
 
==Regression==
 
==Regression==
 
* [http://statgen.us/files/tutorials/regression_exercise.pdf Regression Exercise <nowiki>[PDF]</nowiki>]
 
* [http://statgen.us/files/tutorials/regression_exercise.pdf Regression Exercise <nowiki>[PDF]</nowiki>]
* [[Regression_Exercise|Commands in Exercise]]
+
* [[Regression_Exercise|Exercise Commands]]
 +
 
 +
To install from packages, follow the configuration steps above and run the following command.
 +
 
 +
<pre>sudo apt-get install regression-tutorial</pre>
 +
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.pdf Exercise <nowiki>[PDF]</nowiki>]
[[RVTDT_Commands|Exercise Commands]]
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* [[RV-TDT|Exercise Commands]]
  
 
====Installing Packages====
 
====Installing Packages====
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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.
 
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.
  
==Population Genetics==
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==SEQLinkage==
* [http://statgen.us/files/tutorials/population/Popgen_exe_ans.pdf Popgen Exercise <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/population/popgen_drift.q Commands for popgen_drift]
+
* [[SEQLinkage_Commands_in_Exercise|Exercise Commands]]
* [http://statgen.us/files/tutorials/population/popgen_selection.q Commands for popgen_selection]
+
  
==PSEQ==
+
 
* [http://statgen.us/files/tutorials/pseq/PSEQ_exercise.pdf PSEQ Exercise <nowiki>[PDF]</nowiki>]
+
To install from packages, follow the configuration steps above and run the following command.
* [[PSEQ Commands in Exercise|Commands in Exercise]]
+
 
 +
<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==
 
* [http://statgen.us/files/tutorials/seqspark/SEQSpark_exercise_Final_v4.pdf SEQSpark Exercise <nowiki>[PDF]</nowiki>]
 
* [http://statgen.us/files/tutorials/seqspark/SEQSpark_exercise_Final_v4.pdf SEQSpark Exercise <nowiki>[PDF]</nowiki>]
 +
* [[SEQSpark|Exercise Commands]]
 
* [http://statgen.us/files/images/SEQSpark.ova Virtual Machine Image]
 
* [http://statgen.us/files/images/SEQSpark.ova Virtual Machine Image]
  
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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==
 +
* [http://statgen.us/files/tutorials/seqspark/slink_ex_short.pdf SLINK Exercise <nowiki>[PDF]</nowiki>]
 +
 +
 +
To install from packages, follow the configuration steps above and run the following command.
 +
 +
<pre>sudo apt-get install slink-tutorial</pre>
 +
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==
 +
* [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>]
 
* [http://statgen.us/files/tutorials/VAT_exercise_2018_nographs.pdf VAT Exercise <nowiki>[PDF]</nowiki>]
* [[VAT Commands in Exercise|Commands in Exercise]]
+
* [[VAT Commands in Exercise|Exercise Commands]]
  
 
====Installing Packages====
 
====Installing Packages====
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<pre>sudo apt-get install vtools-tutorial</pre>
 
<pre>sudo apt-get install vtools-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.
 +
 +
==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.
 +
 +
<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 00:45, 25 June 2018

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

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.

Annovar MEndelian

Cochran Armitage Trend Test

GATK and IGV

Software Links

Result Files

Gemini

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

Linkage/FastLinkage

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.

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 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

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.

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.