Here we present a computational pipeline for processing bulk RNA calling card data. These data will have been generated from transfection\/-duction of either undirected piggyBac transposase or your favorite transcription factor (YFTF) fused to piggyBac. Multiple biological replicates should have been generated, each with a unique combination of primer barcode and index sequences. This workflow demonstrates how to analyze a single replicate; the workflow can be parallelized on distributed computing architectures (e.g. slurm).