Project

This project aims at creating a package with multiple tools to analyze Alternative Polyadenylation (APA) from RNA sequencing data (bulk and single-cell).

Installation

To install this library in another Python project, execute simply:

pip install git+https://github.com/idiap/apatools.git

or

git clone https://github.com/idiap/apatools.git
cd apatools
pip install .

Scripts

bulkapa

bulkapa.py aims at performing 3' UTR analysis of bulk RNA sequencing data. To run it, udpate the file config/bulkapa_template.yaml with the right paths. You can then run the script as follows:

python3 scripts/bulkapa.py --config_file config/bulkapa_template.yaml

The config file should contain:

• df_counts_3UTR_path: Path to the matrix of 3' UTR isoforms (output of quantification).
• gtf_file_focus: GTF file used for quantification of the 3' UTR isoforms -- usually it corresponds to a focus on the last nucleotides of the original 3' UTR isoform annotation.
• gtf_file_no_focus: Original GTF file describing the 3' UTR isoforms (no focus on the last nucleotides).
• df_filtered_genes_path: Path to the reliably expressed genes dataframe. Should contain gene names in the first column. This matrix is used to filter the reliably expressed 3' UTR isoforms.
• extension_figures: Extension you want to save your figures with, e.g "pdf", "png",...
• treatments: dictionnary with name of the treatments in keys and list of corresponding sample names in keys.
• path_to_results: Directory where to save the results.