BSGatlas workflow

These are the scripts that were used to create the BSGatlas annotation for Bacillus subtilis strain 168.

“BSGatlas: A Unified Bacillus Subtilis Genome and Transcriptome Annotation Atlas with Enhanced Information Access.”. Geissler, Adrian Sven, Christian Anthon, Ferhat Alkan, Enrique González-Tortuero, Line Dahl Poulsen, Thomas Beuchert Kallehauge, Anne Breüner, Stefan Ernst Seemann, Jeppe Vinther, and Jan Gorodkin.
Microbial Genomics 7, no. 2 (February 4, 2021). https://doi.org/10.1099/mgen.0.000524.

A persistent copy of the code is also available at https://doi.org/10.5281/zenodo.4305872

The folder structure in this project is:

• analysis: R scripts that created the annotation and associated analyses
• data-raw: Utilized external data in their raw form
• data: Parsed form of the external data. Contains both scripts and Rdata objects
• data-hub: Browser hub folder for the final BSGatlas annotation
• data-gff: GFF version of the BSGatlas
• scripts: longer scripts and helper functions that were used

For improved reproducbility, an exact description of the used conda environment is stored in conda.yml with

conda env export > conda.yml

If you wish to recreate this environment, install it and activate it with

conda env create --file cona.yml
conda activate bsgatlas

License

Due to the external resources, this repository's content has mixed licenses.

• The BSGatlas and the scripts that generated it are under the Apache License Version 2.0
• SubtiWiki is provided under the *CC BY 4.0
• DBTBS was provided by the authors Yuko Makita and Kenta Nakai and is subjected to their copyright.
• The use of the BsubCyc annotation is granted by the royality-free and re-distribution allowing proprietary academic license. (Includes BioCycTM pathway/genome databases under license from SRI International)
• The results of the Rfam scan were created as part of the BSGatlas and is thus available under the Apache License Version 2.0
• The RefSeq annotation is in the public domain.
• The data tables from the supplementary materials by Dar et al. and Nicolas et al. are used for the academic useage

Note on Nicolas et al. tiling-array signals

With the BSGatlas v1.1, the signals of Nicolas et al.'s tiling-array experiments were added to the browser hub. Due their massive size, the raw-files are not included in this repository, however, they can easily be reloaded from GEO. If you intend to re-run the script that process the raw data for the browser hub, download the files and recreate the following file hierarchy under data-raw/GEO.

    data-raw/GEO
    ├── GPL8486_family.soft.gz
    ├── GSE27219_RAW
    │   ├── GPL13149_070910_BaSysBio_expr.ndf.gz
    │   ├── GPL13149_070910_BaSysBio_expr.pos.gz
    │   ├── GSM672549.pair.gz
    │   ├── GSM672550.pair.gz
    │   ├── GSM672551.pair.gz
    │   ├── ...
    │   ├── GSM672813.pair.gz
    │   ├── GSM672814.pair.gz
    │   ├── GSM672815.pair.gz
    │   ├── GSM672816.pair.gz
    │   └── GSM672817.pair.gz
    ├── GSE27219_RAW.tar
    └── GSE27219_family.soft.gz