Difference between revisions of "Tutorials"
From Statistical Genetics Courses
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==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>] | ||
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| + | ==Cochran Armitage Trend Test== | ||
| + | * [http://statgen.us/files/tutorials/Armitage_sample_size_Berlin_1.pdf CATT Exercise <nowiki>[PDF]</nowiki>] | ||
| + | |||
| + | ==GATK and IGV== | ||
| + | * [http://statgen.us/files/tutorials/Variant_calling_exercices_GATK_IGV.pdf GATK/IGV Exercise <nowiki>[PDF]</nowiki>] | ||
| + | |||
| + | ====Software Links==== | ||
| + | :* [https://www.broadinstitute.org/gatk/ GATK] | ||
| + | :* [http://www.broadinstitute.org/igv/ IGV] ([http://statgen.us/files/software/igv.jar Download JAR file]) | ||
| + | |||
| + | ====Result Files==== | ||
| + | :* [http://statgen.us/files/2016/07/gatk_results.tar.gz GATK/IGV exercise] | ||
==GenABEL== | ==GenABEL== | ||
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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_DataQC''. 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_DataQC''. You can run from there or copy the files into your user's home directory and proceed with the exercise. | ||
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==GWAS: Association Analysis Controlling for Population Substructure== | ==GWAS: Association Analysis Controlling for Population Substructure== | ||
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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. | ||
| − | + | ==Regression== | |
| + | * [http://statgen.us/files/tutorials/regression_exercise.pdf Regression Exercise <nowiki>[PDF]</nowiki>] | ||
| + | * [[Regression_Exercise|Commands in Exercise]] | ||
==RV-TDT== | ==RV-TDT== | ||
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<pre>sudo apt-get install rvtdt-tutorial</pre> | <pre>sudo apt-get install rvtdt-tutorial</pre> | ||
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== | ||
| + | * [http://statgen.us/files/tutorials/population/Popgen_exe_ans.pdf Popgen Exercise <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] | ||
==PSEQ== | ==PSEQ== | ||
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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. | 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. | ||
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Revision as of 16:36, 6 June 2018
Contents
Running Tutorials on Your Computer
We have created a debian repository to make it easier to use our tutorials. Using this repository will require that you have administrator access to the computer on which you'll be using them. If you don't have this level of access, we also provide a pre-configured virtual machine image that will allow you to install software as root.
The VM Image is available here. The password for the student account is "LetMeIn". Feel free to change it to whatever you like.
If you would like to use our repository on a VM or on your computer, 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 ppa:webupd8team/java sudo apt-get update
Annotation
Functional Annotation Exercise [PDF]
Cochran Armitage Trend Test
GATK and IGV
Software Links
Result Files
GenABEL
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.
Regression
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.
Population Genetics
PSEQ
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.
