prime-vs-base-editing's Introduction

prime-vs-base-editing

This repo contains code used to compare the capabilities of prime editing and base editing to model mutations catalogued in the MSK IMPACT dataset.

Reference files are too large for Github (100 Mb limit), and are available at the following dropbox repository: https://www.dropbox.com/sh/ovbpiswfghlx1j6/AABCfbBUdH-65QMzD6UyQnvwa?dl=0

Information about each notebook present in repo:

Genome Processing_CLEAN.ipynb: A script that creates annotation file for genes represented in the MSK IMPACT dataset.
BE Coverage_CLEAN.ipynb: A script that quantifies the capabilities of base editing (BE) to model mutations present in the MSK IMPACT dataset. Includes some figure generation as well.
PE Coverage_CLEAN.ipynb: A script that quantifies the capabilities of prime editing (PE) to model mutations present in the MSK IMPACT dataset. Includes some figure generation as well.
Mouse_Human_Align_CLEAN.ipynb: A script that generates a global pairwise alignment index between orthologous human and mouse proteins. It also generates a mapping from the DNA level to the amino acid level. The files generated in this notebook are used to determine whether a concordant mutation can be modeled in mouse in the following notebook (Mouse_Human_Mutation_Modeling_CLEAN.ipynb).
Mouse_Human_Mutation_Modeling_CLEAN.ipynb: A script that determines whether a concordant mutation can be modeled in mouse at varying stringencies/requirements for the homology of the region flanking the mutation of interest.
Figure creation_CLEAN.ipynb: Contains figures generated to visualize homology, as well as other miscellaneous figures not present in PE Coverage/BE Coverage notebooks.
Supplement figures_CLEAN.ipynb: Notebook used to generate supplementary figures. Includes analysis of prime vs. base editing capabilities when looking at recurrent mutations, and when using different stringencies of homology between human and mouse.