PEPPRO is a pipeline for nascent RNA sequencing data. It can process PRO-seq, GRO-seq, and ChRO-seq data and is optimized on unique features of nascent RNA to be fast and accurate. It performs variable-length UMI adapter removal, read deduplication, trimming, mapping, QC, and signal tracks (bigWig) for plus and minus strands using mappability-scaled or unscaled read counts.
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Smith JP, Dutta AB, Sathyan KM, Guertin MJ, Sheffield NC.
PEPPRO: quality control and processing of nascent RNA profiling data.
Genome Biol. 2021 May 15;22(1):155. doi: 10.1186/s13059-021-02349-4. PMID: 33992117; PMCID: PMC8126160.