TRACEseq Code

This repository contains the code associated with Sharma et al. Nature Communications 2021

link to paper

The code in the repository generates all bubble plots shown in the publication (Figures 4,5,Extended Figures 3,5).

To run the code:

1. Download or clone the repository locally.
2. Open generate_bubble_plots.R in Rstudio.
3. Navigate to the local directory containing the repository code.
4. Run code (this will source bubble_plot_functions.R and generate all plots)

The following libraries must be installed for the code to function.

• openxlsx
• ggpubr
• packcircles
• ggplot2
• grid

The script align_and_filter_pre_tuba_HBB.py is utilized in our analyses within the TUBAseq pipeline as described in the manuscript. The script filters a fastq file and bins reads into HR, NHEJ, Unmodified, and Other categories.