Streamline the assignment of ATAC peaks to cis-regulatory regions, facilitating links between these regions and genes.
This repository contains Python functions designed to work with Python 3 (tested with Python 3.9, 3.10, and 3.11). To utilize these functions, ensure you have the pybedtools library installed. For installation options, please refer to the official documentation at pybedtools.
Stay tuned for the forthcoming conda environment, which will further simplify the setup process.
The get_tss.py script is essential for the initial processing of cis-reg annotations. It extracts transcription start sites (TSS) from a provided GFF3 file, and converts this information into BED format for further analysis. This script supports output customization through command-line arguments, allowing users to either save the results to a file or print them directly to the console. This utility is critical for preparing the data needed for downstream regulatory mapping.
Usage:
python get_tss.py -i your_input_file.gff3 -o your_output_file.bedThe cisreg_map.py script is a comprehensive tool for mapping ATAC peaks to specific putative cis-regulatory regions within a genome. It categorizes genomic regions into promoters, proximal areas, and gene bodies based on definitions specified:
- Promoter: Defined as 1000 bases upstream and 500 bases downstream of the TSS.
- Proximal Region: Defined as the area extending 4000 bases from the TSS but not overlapping with the promoter.
- Gene Body: Defined as the part of the gene that is not included in the promoter.
This script utilizes input files detailing TSS, genes, and peaks in BED format, alongside a length file. It not only outputs tables linking peaks with genes and putative cis-regulatory regions but also includes a detailed summary of how each putative cis-regulatory region was defined, offering insights into the genomic landscape of regulation.
Usage:
python cisreg_map.py -t your_tss_file.bed -g your_genes_file.bed -p your_peaks_file.bed -l your_length_file.txt -o your_output_file_prefixFor more information or support, please contact Maria Rossello at mariarossello@ub.edu.