READ ME FIRST!!! MaChIAto (Microhomology-associated Chromosomal Integration/editing Analysis tools); a comprehensive analysis software that can precisely classify, deeply analyze, correctly align, and thoroughly review the targeted amplicon s...
Quick Start
We demonstrate a simple example. 1. Download MaChIAto with example filesEnter the following command terminal after you download and install Docker Desktop: https://docs.docker.com/engine/install/#desktop. 12# Download Docker image for MaChIAto Cla...
Preparation
The MaChIAto consists of python and R with various packages other developers established. So the installation process is complex. However, you can quickly install MaChIAto using the docker container. Install MaChIAto using the docker (Strongly Rec...
How to evaluate MaChIAto using ART
We used the following script to evaluate MaChIAto classification in the manuscript. The evaluation is based on the markrobinsonuzh/CrispRvariants_manuscript. We modified it to generate our evaluation data. MainScript 12345678910111213141516...
Usage of collect_MaChIAto_data.py
The user should execute collect_MaChIAto_data.py to make input file of MaChIAto Analyzer and MaChIAto Reviewer Parameter list-i or –indir {str}: input directory which includes the outputs of MaChIAto Classifier -o or –outdir {str}: output director...
How to calculate the value of accessibility
We used the following script to calculate the value of accessibility.First, we find the region coordinates on which we focused using Blat search and then executed the script. 123456789101112131415161718192021222324252627282930313233343536373839404...
Output of MaChIAto Reviewer
[Coming soon]
Usage of MaChIAto Reviewer
Parameter listSummary directory:The summary directory generated with “collect_MaChIAto_data.py”. Output prefix:The directory into which the output directory is saved. Template commandRscript MaChIAto_Reviewer/MaChIAtoReviewer.R (Summary direc...
Output of MaChIAto Analyzer
[Coming soon]