This pipeline functions to quantify levels of alternative polyadenylation (APA) using the QAPA package released by Ha, Blencowe and Morris (2018). The output from QAPA consists of a database containing individual sample APA quantifications. Custom python and R scripts are used to interogate this database and subsequently allow for multiple comparisons to be made based on the design.tsv (see below).
To execute this pipeline in an interactive ShARC session or from a personal device (not recommended) use the following command:
python <path_to_pipeline_folder>/pipeline_QAPA.py make full -v5
To execute this pipeline to the ShARC cluster, use the following:
submit_pipeline <path_to_pipeline_folder>/pipeline_QAPA.py make full -v5