Beat - Base Editing Analysis Tool

Beat determines editing efficiency after subtracting the background noise without the need to normalize to control samples. It finds the noise and filters the outliers from the noise using the Median Absolute Deviation (MAD) method

Usage

The usage:

python Beat.py [--data-path] [--filename|all] [--spacer] [-base-change-position] [--change-pattern] 

or for the batch analysis:

python Beat.py [--csv-path]

Example

To run batch analysis:

python Beat.py ./data all GAGTATGAGGCATAGACTGC 5 AG

to analyze all sequencing files if they have the same spacer. And if they contain different spacers, just run as

python Beat.py ./data/template1.csv 

To analyze individual sequencing file, run

python Beat.py ./data Site2_PCR_420.ab1 GAGTATGAGGCATAGACTGC 5 AG

Dependency

To install the necesssary packages, run:

pip install biopython pandas numpy scipy openpyxl

The Executable file

To download the .exe file, please use this link:

https://drive.google.com/open?id=13NvLL70i7sTlNw04FF_n4b-RxFndlovw