Usage of MaChIAto Aligner
Parameter list
Input directory:
The directory that MaChIAto Classifier generated.
Output prefix:
The directory into which the output directory is saved.
Left extra sequence (optional):
The outside sequence flanking 5’-homology arm of the donor.
Right extra sequence (optional):
The outside sequence flanking 3’-homology arm of the donor.
Template command
1
2
3
4
5
| Rscript MaChIAto_Aligner/MaChIAtoAligner.R \
(Input directory) \
(Output prefix) \
(Left extra sequence) \
(Right extra sequence);
|
*when you use external storage for save output, the process can be too slow. We recommend that you use the tool in the local storage.
Example of the command
Here is example of the command using docker.
If you don’t have the docker image for MaChIAto Aligner, please go the Preparation page: https://machiatopage.github.io/2100/01/01/Preparation/
The input file can be downloaded from the following link:
https://sourceforge.net/projects/machiato-example-files/files/example_MaChIAtoClassifier_docker_output.zip/download
You can check the output file of the below examples following the following link:
https://sourceforge.net/projects/machiato-example-files/files/example_MaChIAtoAligner_docker_output.zip/download
Case of knock-out
1
2
3
| docker run --rm -v `pwd`:/DATA -w /DATA -i kazukinakamae/machiato_aligner:latest Rscript ../MaChIAtoAligner.R \
example_MaChIAtoClassifier_docker_output/MaChIAto_from_CRISPResso2_at_20220712042914_on_AAVS1-KO \
example_MaChIAtoAligner_docker_output;
|
1
2
3
| docker run --rm -v `pwd`:/DATA -w /DATA -i kazukinakamae/machiato_aligner:latest Rscript ../MaChIAtoAligner.R \
example_MaChIAtoClassifier_docker_output/MaChIAto_from_CRISPResso2_at_20220712043728_on_CD40LG-KO \
example_MaChIAtoAligner_docker_output;
|
1
2
3
| docker run --rm -v `pwd`:/DATA -w /DATA -i kazukinakamae/machiato_aligner:latest Rscript ../MaChIAtoAligner.R \
example_MaChIAtoClassifier_docker_output/MaChIAto_from_CRISPResso2_at_20220712043751_on_DBF4B-KO \
example_MaChIAtoAligner_docker_output;
|
1
2
3
4
5
| docker run --rm -v `pwd`:/DATA -w /DATA -i kazukinakamae/machiato_aligner:latest Rscript ../MaChIAtoAligner.R \
example_MaChIAtoClassifier_docker_output/MaChIAto_from_CRISPResso2_at_20220712043845_on_AAVS1-KI \
example_MaChIAtoAligner_docker_output \
GTTTGG \
CCAAAC;
|
1
2
3
4
5
| docker run --rm -v `pwd`:/DATA -w /DATA -i kazukinakamae/machiato_aligner:latest Rscript ../MaChIAtoAligner.R \
example_MaChIAtoClassifier_docker_output/MaChIAto_from_CRISPResso2_at_20220712043906_on_CD40LG-KI \
example_MaChIAtoAligner_docker_output \
GTTTGG \
CCAAAC;
|
1
2
3
4
5
| docker run --rm -v `pwd`:/DATA -w /DATA -i kazukinakamae/machiato_aligner:latest Rscript ../MaChIAtoAligner.R \
example_MaChIAtoClassifier_docker_output/MaChIAto_from_CRISPResso2_at_20220712043917_on_DBF4B-KI \
example_MaChIAtoAligner_docker_output \
GTTTGG \
CCAAAC;
|
Case of untreated sample for negative control (Optional)
1
2
3
| docker run --rm -v `pwd`:/DATA -w /DATA -i kazukinakamae/machiato_aligner:latest Rscript ../MaChIAtoAligner.R \
example_MaChIAtoClassifier_docker_output/MaChIAto_from_CRISPResso2_at_20220712043934_on_AAVS1-WT \
example_MaChIAtoAligner_docker_output;
|
1
2
3
| docker run --rm -v `pwd`:/DATA -w /DATA -i kazukinakamae/machiato_aligner:latest Rscript ../MaChIAtoAligner.R \
example_MaChIAtoClassifier_docker_output/MaChIAto_from_CRISPResso2_at_20220712043951_on_CD40LG-WT \
example_MaChIAtoAligner_docker_output;
|
1
2
3
| docker run --rm -v `pwd`:/DATA -w /DATA -i kazukinakamae/machiato_aligner:latest Rscript ../MaChIAtoAligner.R \
example_MaChIAtoClassifier_docker_output/MaChIAto_from_CRISPResso2_at_20220712044004_on_DBF4B-WT \
example_MaChIAtoAligner_docker_output;
|
1
2
3
4
5
| docker run --rm -v `pwd`:/DATA -w /DATA -i kazukinakamae/machiato_aligner:latest Rscript ../MaChIAtoAligner.R \
example_MaChIAtoClassifier_docker_output/MaChIAto_from_CRISPResso2_at_20220712044026_on_AAVS1-KI2 \
example_MaChIAtoAligner_docker_output \
GTTTGG \
CCAAAC;
|
1
2
3
4
5
| docker run --rm -v `pwd`:/DATA -w /DATA -i kazukinakamae/machiato_aligner:latest Rscript ../MaChIAtoAligner.R \
example_MaChIAtoClassifier_docker_output/MaChIAto_from_CRISPResso2_at_20220712044040_on_CD40LG-KI2 \
example_MaChIAtoAligner_docker_output \
GTTTGG \
CCAAAC;
|
1
2
3
4
5
| docker run --rm -v `pwd`:/DATA -w /DATA -i kazukinakamae/machiato_aligner:latest Rscript ../MaChIAtoAligner.R \
example_MaChIAtoClassifier_docker_output/MaChIAto_from_CRISPResso2_at_20220712044052_on_DBF4B-KI2 \
example_MaChIAtoAligner_docker_output \
GTTTGG \
CCAAAC;
|
