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. | ||
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. | + | <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> | ||
− | + | 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. | |
− | < | + | ==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/ | + | * [http://statgen.us/files/tutorials/functional-annotation/FunctionalAnnotation_exercise_2019.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== | ||
− | * [http://statgen.us/files/tutorials/ | + | * [http://statgen.us/files/tutorials/Armitage_sample_size_revised.pdf CATT Exercise <nowiki>[PDF]</nowiki>] |
==GATK and IGV== | ==GATK and IGV== | ||
Line 31: | Line 44: | ||
====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/ | + | * [http://statgen.us/files/tutorials/gwas-qc/PLINK_data_QC_V2.pdf Exercise <nowiki>[PDF]</nowiki>] |
− | * [[GWAS Data QC Exercise| | + | * [[GWAS Data QC Exercise|Exercise Commands]] |
====Installing Packages==== | ====Installing Packages==== | ||
Line 47: | Line 78: | ||
==GWAS: Association Analysis Controlling for Population Substructure== | ==GWAS: Association Analysis Controlling for Population Substructure== | ||
− | * [http://statgen.us/files/tutorials/gwas-substructure/ | + | * [http://statgen.us/files/tutorials/gwas-substructure/GWAS_Data_Controlling_for_Substructure_V2.pdf Exercise <nowiki>[PDF]</nowiki>] |
− | * [[GWAS_Controlling_for_Population_Substructure| | + | * [[GWAS_Controlling_for_Population_Substructure|Exercise Commands]] |
====Installing Packages==== | ====Installing Packages==== | ||
Line 55: | Line 86: | ||
<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_2019.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| | + | * [[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/ | + | * [http://statgen.us/files/tutorials/rvtdt/rvtdt_exercise_v3.pdf Exercise <nowiki>[PDF]</nowiki>] |
− | * [[RV-TDT| | + | * [[RV-TDT|Exercise Commands]] |
====Installing Packages==== | ====Installing Packages==== | ||
Line 70: | Line 139: | ||
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. | ||
− | == | + | ==SEQLinkage== |
− | * [http://statgen.us/files/tutorials/ | + | * [http://statgen.us/files/tutorials/SEQLinkage/SEQLinkage_revised_with_pg_numb.pdf SEQLinkage Exercise <nowiki>[PDF]</nowiki>] |
− | * [ | + | * [[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== | ||
* [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| | + | * [[SEQSpark|Exercise Commands]] |
* [http://statgen.us/files/images/SEQSpark.ova Virtual Machine Image] | * [http://statgen.us/files/images/SEQSpark.ova Virtual Machine Image] | ||
Line 90: | Line 160: | ||
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/ | + | * [http://statgen.us/files/tutorials/vat/VAT_exercise_2019_1_nographs.pdf VAT Exercise <nowiki>[PDF]</nowiki>] |
− | * [[VAT Commands in Exercise|Commands | + | * [[VAT Commands in Exercise|Exercise Commands]] |
====Installing Packages==== | ====Installing Packages==== | ||
Line 99: | Line 182: | ||
<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 17:28, 19 June 2019
Contents
- 1 Running Tutorials on Your Computer
- 2 Alohomora
- 3 Annotation
- 4 Annovar MEndelian
- 5 Cochran Armitage Trend Test
- 6 GATK and IGV
- 7 Gemini
- 8 GenABEL
- 9 Genehunter
- 10 GWAS: Data Quality Control
- 11 GWAS: Association Analysis Controlling for Population Substructure
- 12 Homozygosity Mapper
- 13 IGV
- 14 Linkage/FastLinkage
- 15 Population Genetics
- 16 PSEQ
- 17 Regression
- 18 RV-TDT
- 19 SEQLinkage
- 20 SEQSpark
- 21 SLINK
- 22 SUPERLINK
- 23 Variant Association Tools
- 24 VAT Mendelian
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 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.