PEPPRO

PEPPRO processes nascent RNA sequencing data to perform preprocessing, quality control, and signal track generation for GRO-seq, PRO-seq, and ChRO-seq experiments.

Key Features:

• Data Processing Capabilities: Supports variable-length UMI adapter removal, read deduplication, trimming, and mapping optimized for nascent RNA data.
• Quality Control Metrics: Calculates adapter abundance, RNA integrity, library complexity, nascent RNA purity, and run-on efficiency.
• Signal Track Generation: Produces bigWig signal tracks for plus and minus strands with optional mappability-scaled or unscaled read counts.
• Scalability and Portability: Enables scalable execution on local machines or computing clusters for standardized preprocessing of nascent RNA datasets.
• Fault Tolerance and Logging: Provides restartable, fault-tolerant execution with extensive logging for reproducibility and troubleshooting.

Scientific Applications:

• Nascent transcription profiling: Processes GRO-seq, PRO-seq, and ChRO-seq data to profile nascent RNA.
• Transcription dynamics and regulation: Supports analyses of transcription dynamics and regulatory mechanisms.
• Chromatin interaction and run-on assessment: Facilitates studies of chromatin interactions and assessment of run-on efficiency.

Methodology:

Performs variable-length UMI adapter removal, read deduplication, trimming, mapping, calculation of quality control metrics, and generation of bigWig signal tracks with optional mappability scaling.