Manual alignment of short E. coli genes to sequencing data

This repository contains the code used to manually align RNA-Seq reads to short (<100nt) genes in the E. coli genome that are typically misreported by RNA-Seq algorithms to have zero read counts. The data 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 3.11.3. After installing Python, you can install all of the required packages by running

pip install -r requirements.txt

To regenerate all short gene alignment data used in Sun et al. (2024), run

bash runscripts/align_short_genes.sh