Base-editing evaluation program (BEEP)
This protocol is extracted from research article:
Minimal PAM specificity of a highly similar SpCas9 ortholog
Sci Adv, Oct 24, 2018; DOI: 10.1126/sciadv.aau0766

The BEEP software was written in Python, using the pandas data manipulation library and BioPython package. As inputs, the program requires a sample ab1 file, a negative control ab1 file, a target sequence, and the position of the specified base conversion, handled as a.csv file either for multiple sample analysis or for individual samples on the command line. Briefly, the provided target sequences are aligned to the base calls of each input ab1 file to determine the absolute position of the target within the file. Subsequently, the peak values for each base at the indicated position in the spacer are obtained, and the editing percentage of the specified base conversion is calculated. Last, a separate function normalizes the editing percentage to that of the negative control ab1 file to account for background signals of each base. The final base conversion percentage is outputted to the same .csv file for downstream analysis. The BEEP software can be downloaded at https://github.com/mitmedialab/BEEP.

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