/BEEP

Base Editing Evaluation Program

Primary LanguagePythonMIT LicenseMIT

BEEP

Base Editing Evaluation Program

Assessing CRISPR-mediated base editing efficiency from Sanger sequencing ab1 files

Dependencies

  1. pandas
pip install pandas
  1. Biopython
pip install Biopython

What You Need

  1. beep.py
  2. Negative control of amplified region: control.ab1 file
  3. Sample ab1 files
  4. .csv file containing ab1 file names, target sequences, base position in target, and desired base conversion (template provided)

Installation

git clone https://github.com/mitmedialab/BEEP

Running BEEP

To run multiple samples at once:

python beep.py ./example/template.csv

To run a single sample:

python beep.py folder_with_ab1s control.ab1 sample.ab1 target_sequence base_position base_conversion

Example:

python beep.py example control.ab1 sample.ab1 TCGGCCACCACAGGGAAGCT 6 CT

Output

  • Efficiences will be outputted to the provided .csv file under "Efficiency" header, or in the terminal for single sample usage.
  • .png files are created with edits visualized as chromatograms.

Author

Pranam Chatterjee