This repository contains demo code for the manuscript: "Nucleotide-Resolution Mapping of Regulatory Elements via Allelic Readout of Tiled Base Editing"

Specifically, the code demos the following core packages:

• CRISPR-Millipede for processing targeted amplicon-sequencing of tiled sequences from base-editing tiling screens to identify functional nucleotides
• CRISPR-Correct for performing guide RNA mapping given the raw FASTQs and guide library dataframe.
• CRISPR-SURF from Hsu et al., Nature Methods 2018 for the design and analysis of CRISPR-Cas, CRISPRi, and CRISPRa tiling screens.

See the following Zenodo for the full ZIP file contain all code and data (data is not included in GitHub due to file size constraints): https://doi.org/10.5281/zenodo.13737736