Rend-seq-plots

This repository contains the data and code that is necessary to visualize the end-enriched RNA sequencing (Rend-seq) data reported by Lalanne et al. (2018). The plots generated by the code were used as supporting figures for Sun et al., "Cross-evaluation of E. coli’s operon structures via a whole-cell model suggests alternative cellular benefits for low- versus high-expressing operons", Cell Systems, 2024.

You can reach out to ggsun AT stanford.edu for any questions about the code in this repository.

This repository was developed with Python 3.8.7. After installing Python, you can install all of the required packages by running

pip install -r requirements.txt

To regenerate all Rend-seq figures used in Sun et al. (2024), run

bash runscripts/paper_figures.sh