This pipeline processes sequencing data from Massively Parallel Reporter Assays (MPRAs) to create count tables for candidate sequences tested in the experiment.

This package contains three utilities:

ASSIGNMENT (previous associations)

This utility takes in library association sequencing data (FASTQ) and a design file (FASTA) to assign barcodes to the corresponding elements tested. Functionality includes filtering for quality and coverage of barcodes. This utility must be run before the Experiment (Count) utility. See Assignment for more details.

EXPERIMENT (previous count)

This utility processes sequence data (FASTQ) of barcodes from the DNA and RNA fractions of the MPRA experiment and outputs count tables labeled with the element tested and a label provided in the design file. This utility can process multiple replicates and conditions in a parallelized manner. Based on a user specified flag, the pipeline will either output normalized activity for each tested sequence, or will combine the results into a single count matrix compatible with MPRAnalyze. See Experiment (Count) for more details.