This archive contains the Snakemake workflow as it was used in the Genome Biology publication. The workflow is provided in a self-contained environment that only requires Conda and Snakemake to be executed. It connects the PAQR and KAPAC modules and includes as example input the mapped RNA-seq samples from the study of HNRNPC knock-down in HEK293 cells (originally published on the GEO database with the accession number GSE56010), available also from here: http://www.clipz.unibas.ch/RNAseq_HNRNPC_KD_study. PAQR is a method for polyadenylation site usage quantification from RNA sequencing data. KAPAC infers position-dependent activities of sequence motifs on 3’ end processing from changes in poly(A) site usage between conditions.