Usage of MaChIAto Reviewer

Parameter list

Summary directory:
The summary directory generated with “collect_MaChIAto_data.py”.

Output prefix:
The directory into which the output directory is saved.

Template command

Rscript MaChIAto_Reviewer/MaChIAtoReviewer.R
(Summary directory)
(Output prefix);

Example of the command

Here is example of the command using docker.

If you don’t have the docker image for MaChIAto Reviewer, please go the Preparation page: https://machiatopage.github.io/2100/01/01/Preparation/

The input file can be downloaded from the following link:
MaChIAto Classifier: https://sourceforge.net/projects/machiato-example-files/files/example_MaChIAtoClassifier_docker_output.zip/download
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: knock-out using MS2-tagged sgRNA/calculation target: protospacer

docker run --rm -v `pwd`:/DATA -w /DATA -i kazukinakamae/machiato_reviewer:latest Rscript ../MaChIAtoReviewer.R \
example_MaChIAtoClassifier_docker_output \
example_MaChIAtoAligner_docker_output \
collections/Simple_knockout_analysis \
example_MaChIAtoReviewer_docker_output;

Output: https://sourceforge.net/projects/machiato-example-files/files/example_MaChIAtoReviewer_docker_output/MaChIAtoReviewer_at_20220723205931%28Simple%20knock-out%20analysis%29.zip/download

Single knock-out analysis: knock-out using MS2-tagged sgRNA/calculation target: protospacer

docker run --rm -v `pwd`:/DATA -w /DATA -i kazukinakamae/machiato_reviewer:latest Rscript ../MaChIAtoReviewer.R \
example_MaChIAtoClassifier_docker_output \
example_MaChIAtoAligner_docker_output \
collections/Single_knockout_analysis \
example_MaChIAtoReviewer_docker_output;

Output: https://sourceforge.net/projects/machiato-example-files/files/example_MaChIAtoReviewer_docker_output/MaChIAtoReviewer_at_20220723210032%28Single%20knock-out%20analysis%29.zip/download

Double knock-out analysis: MS2-tagged sgRNA/calculation target: protospacer

docker run --rm -v `pwd`:/DATA -w /DATA -i kazukinakamae/machiato_reviewer:latest Rscript ../MaChIAtoReviewer.R \
example_MaChIAtoClassifier_docker_output \
example_MaChIAtoAligner_docker_output \
collections/Double_knockout_analysis \
example_MaChIAtoReviewer_docker_output;

Output: https://sourceforge.net/projects/machiato-example-files/files/example_MaChIAtoReviewer_docker_output/MaChIAtoReviewer_at_20220723205507%28Double%20knock-out%20analysis%29.zip/download

Simple knock-in analysis: PITCh using MS2-tagged sgRNA/calculation target: both homology arm

docker run --rm -v `pwd`:/DATA -w /DATA -i kazukinakamae/machiato_reviewer:latest Rscript ../MaChIAtoReviewer.R \
example_MaChIAtoClassifier_docker_output \
example_MaChIAtoAligner_docker_output \
collections/Simple_knockin_analysis \
example_MaChIAtoReviewer_docker_output;

Output: https://sourceforge.net/projects/machiato-example-files/files/example_MaChIAtoReviewer_docker_output/MaChIAtoReviewer_at_20220723210144%28Simple%20knock-in%20analysis%29.zip/download

Single knock-in analysis: PITCh using MS2-tagged sgRNA/calculation target: both homology arm

docker run --rm -v `pwd`:/DATA -w /DATA -i kazukinakamae/machiato_reviewer:latest Rscript ../MaChIAtoReviewer.R \
example_MaChIAtoClassifier_docker_output \
example_MaChIAtoAligner_docker_output \
collections/Single_knockin_analysis \
example_MaChIAtoReviewer_docker_output;

Output: https://sourceforge.net/projects/machiato-example-files/files/example_MaChIAtoReviewer_docker_output/MaChIAtoReviewer_at_20220723210352%28Single%20knock-in%20analysis%29.zip/download

Double knock-in analysis: PITCh and LoAD knock-in using MS2-tagged sgRNA/calculation target: both homology arm

docker run --rm -v `pwd`:/DATA -w /DATA -i kazukinakamae/machiato_reviewer:latest Rscript ../MaChIAtoReviewer.R \
example_MaChIAtoClassifier_docker_output \
example_MaChIAtoAligner_docker_output \
collections/Double_knockin_analysis \
example_MaChIAtoReviewer_docker_output;

Output: https://sourceforge.net/projects/machiato-example-files/files/example_MaChIAtoReviewer_docker_output/MaChIAtoReviewer_at_20220723210653%28Double%20knock-in%20analysis%29.zip/download