Example

To quickly get started with ATACofthesnake, functionality to download and play around with example data is provided. This data is publicly available, and was generated by Yoshida et al. (immgen) [1] and Gaidatzis et al. (cele) [2]. The first dataset contains time series data in C. elegans, the second dataset contains data from the developing T-cell lineage in mice. To download the data, the following command can be used:

ATAC_example -h

By default both datasets will be downloaded. In case you are interested in only one, a positional argument can be used:

ATAC_example immgen

or

ATAC_example cele

An output directory can be specified by using -o or –outputdir. By default, the data will be downloaded a subdirectory ‘aos_example’ in the current working directory. Per project, the cram files will be downloaded, the gene models, fasta file and rar file. For both datasets, a motif file, samplesheet and comparison file are available as well. These can be used as examples for the different differential modes available. Finally, the original accessions for all samples included are available in a text file too, which can be used to retrieve the raw unaligned fastq files from the original repositories, if desired.

References

[1]

Yoshida, H., Lareau, C. A., Ramirez, R. N., Rose, S. A., Maier, B., Wroblewska, A., Desland, F., Chudnovskiy, A., Mortha, A., Dominguez, C., Tellier, J., Kim, E., Dwyer, D., Shinton, S., Nabekura, T., Qi, Y., Yu, B., Robinette, M., Kim, K.-W., … Benoist, C. (2019). The cis-Regulatory Atlas of the Mouse Immune System. Cell, 176(4), 897-912.e20. https://doi.org/10.1016/j.cell.2018.12.036

[2]

Gaidatzis, D., Graf-Landua, M., Methot, S. P., Wölk, M., Brancati, G., Hauser, Y. P., Meeuse, M. W. M., Nahar, S., Braun, K., van der Does, M., Aluri, S., Kohler, H., Smallwood, S., & Großhans, H. (2025). A scheduler for rhythmic gene expression. Molecular Systems Biology, 21(12), 1793–1821. https://doi.org/10.1038/s44320-025-00155-9