Assessing CRISPR-mediated base editing efficiency from Sanger sequencing ab1 files
- pandas
pip install pandas
- Biopython
pip install Biopython
- beep.py
- Negative control of amplified region: control.ab1 file
- Sample ab1 files
- .csv file containing ab1 file names, target sequences, base position in target, and desired base conversion (template provided)
git clone https://github.com/mitmedialab/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
- 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.
Pranam Chatterjee