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Computational supplement for Skalenko et al. (2021)

This repository contains analysis scripts and processed data for,

Skalenko et al. (2021) "Promoter sequence determinants and structural basis of primer dependent transcription initiation in Escherichia coli". bioRxiv doi:10.1101/2021.04.06.438613, Proc. Natl. Acad. Sci. USA. In press.

To reproduce the computational analyses in this manuscript, execute the following iPython notebooks in this order.

  • 1_efficiency.ipynb
  • 2_mixture_modeling.ipynb
  • 3_compute_invivo_logos.ipynb
  • 4_compute_invitro_logos.ipynb
  • 5_compute_chromosomal_logo.ipynb

Using pre-processed data in data/, these scripts will perform analyses and write the results to CSV files in csv_results/ and csv_logos/. To then create select figure panels, execute the following iPython notebooks.

  • fig_3A_oh_pct_table.ipynb
  • fig_4_invivo_invitro_logos.ipynb
  • fig_6A_chromosomal_logo.ipynb
  • fig_S1A_mixture.ipynb
  • fig_S5_invivo_logos_by_primer.ipynb
  • fig_S6_low_hi_invitro_logos.ipynb
  • fig_S8_profiles.ipynb

The resulting graphics will be written to figures/. Note that all output directories are already populated with the output of these analyses.

Please address technical questions about this repository and its contents to Justin B. Kinney. More general scientific correspondence about this work should be sent to Bryce Nickels.


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