Key resources table.

REAGENT or RESOURCE	SOURCE	IDENTIFIER
Deposited data
Rend-seq data	Lalanne et al., 2018	GEO (accession number: GSE95211)
Raw RNA-Seq reads for manual alignment	Macklin et al., 2020	GEO (accession number: GSE85472)
EcoCyc v26.5	Keseler et al., 2021	https://ecocyc.org
Read counts for short genes calculated by the manual alignment algorithm	This paper	Table S1
Software and algorithms
Updated E. coli whole-cell model	This paper	https://github.com/CovertLab/wcEcoli/tree/operon-paper (Zenodo: https://doi.org/10.5281/zenodo.10553485)
Rend-seq analysis scripts	This paper	https://github.com/CovertLab/Rend-seq-plots (Zenodo: https://doi.org/10.5281/zenodo.10553481)
Manual alignment of RNA-Seq reads	This paper	https://github.com/CovertLab/short-gene-alignment (Zenodo: https://doi.org/10.5281/zenodo.10553496)
Non-negative least squares (scipy)	Lawson and Handson, 1987	https://scipy.org/install/