Usage of MaChIAto Analyzer
Parameter list
Summary directory:
The summary directory generated with “collect_MaChIAto_data.py”.
Output prefix:
The directory into which the output directory is saved.
Name of extra data (optional):
The name of the feature group that the next argument includes.
Table of extra data (optional):
The pathname of extra data added by the user. The data should be a .csv file.
Template command
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| Rscript MaChIAto_Analyzer/MaChIAtoAnalyzer.R \
(Summary directory) \
(Output prefix) \
(Name of extra data) \
(Table of extra data);
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Example of the command
Here is example of the command using docker.
If you don’t have the docker image for MaChIAto Analyzer, please go the Preparation page: https://machiatopage.github.io/2100/01/01/Preparation/
The input file can be downloaded from the following link:
MaChIAto Aligner: https://sourceforge.net/projects/machiato-example-files/files/example_MaChIAtoAligner_docker_output.zip/download
Collections of collect_MaChIAto_data.py output: https://sourceforge.net/projects/machiato-example-files/files/collections.zip/download
Simple knock-out analysis: MS2-tagged sgRNA/calculation target: protospacer
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| docker run --rm -v `pwd`:/DATA -w /DATA -i kazukinakamae/machiato_analyzer:latest Rscript ../MaChIAtoAnalyzer.R \
collections/Simple_knockout_analysis \
example_MaChIAtoAnalyzer_docker_output;
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Single knock-out analysis: knock-out using MS2-tagged sgRNA/calculation target: protospacer
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| docker run --rm -v `pwd`:/DATA -w /DATA -i kazukinakamae/machiato_analyzer:latest Rscript ../MaChIAtoAnalyzer.R \
collections/Single_knockout_analysis \
example_MaChIAtoAnalyzer_docker_output;
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Double knock-out analysis: MS2-tagged sgRNA/calculation target: protospacer
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| docker run --rm -v `pwd`:/DATA -w /DATA -i kazukinakamae/machiato_analyzer:latest Rscript ../MaChIAtoAnalyzer.R \
collections/Double_knockout_analysis \
example_MaChIAtoAnalyzer_docker_output;
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Simple knock-in analysis: PITCh using MS2-tagged sgRNA/calculation target: both homology arm
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| docker run --rm -v `pwd`:/DATA -w /DATA -i kazukinakamae/machiato_analyzer:latest Rscript ../MaChIAtoAnalyzer.R \
collections/Simple_knockin_analysis \
example_MaChIAtoAnalyzer_docker_output;
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Single knock-in analysis: PITCh using MS2-tagged sgRNA/calculation target: both homology arm
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| docker run --rm -v `pwd`:/DATA -w /DATA -i kazukinakamae/machiato_analyzer:latest Rscript ../MaChIAtoAnalyzer.R \
collections/Single_knockin_analysis \
example_MaChIAtoAnalyzer_docker_output;
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Double knock-in analysis: PITCh and LoAD knock-in using MS2-tagged sgRNA/calculation target: both homology arm
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| docker run --rm -v `pwd`:/DATA -w /DATA -i kazukinakamae/machiato_analyzer:latest Rscript ../MaChIAtoAnalyzer.R \
collections/Double_knockin_analysis \
example_MaChIAtoAnalyzer_docker_output;
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| docker run --rm -v `pwd`:/DATA -w /DATA -i kazukinakamae/machiato_analyzer:latest Rscript ../MaChIAtoAnalyzer.R \
collections/Double_knockin_analysis \
example_MaChIAtoAnalyzer_docker_output \
InDelphi \
additional_data/bmh_extra_data_InDelphi.csv \
Accessibility \
additional_data/bmh_extra_data_accessibility.csv \
Genome_Property \
additional_data/bmh_extra_data_genomeprop.csv;
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