Gbn-the-SNP-publication-scripts

Data analysis scripts in the article:

Du, C., Willemse, J., Erkelens, A.M., Carrion, V.J., Dame, R.T., and Wezel, G.P.v. (2022) System-wide analysis of the GATC-binding nucleoid-associated protein Gbn and its impact on Streptomyces development. mSystems: e00061-00022.

doi: 10.1128/msystems.00061-22

Dependencies

If you do not want to run the code, please ignore this section.

Recommanded environment:

Linux, WSL2

Partially compatible with windows (lack bedtools) and Mac (lfcShrink).

Oleveler

v1.0 - https://gitlab.services.universiteitleiden.nl/ibl-bioinformatic/oleveler

Commit used:

https://gitlab.services.universiteitleiden.nl/ibl-bioinformatic/oleveler/-/tree/8b848a6e9406d9e82a896bca5934661d71629dc6

ChIP_Expression.py

• bedtools
• pip:
  • pybedtools
  • biopython
  • bcbio-gff
  • matplotlib
  • pandas
  • scipy
  • scikit-learn
  • jupyter lab
  • jupyterthemes

Notes

Re-analysis of transcriptomics data on a Mac system is not possile for unknown incompatibility
of lfcShrink function in DESeq2 package. You may try older versions of R instead (<4.1.2).