Awesome Nascent RNA-seq analysis

A collection of tools, pipelines, and guides for performing nascent RNA sequencing analysis

Raw data processing pipelines

• Nascent-Flow: Nextflow Implementation of the Dowell Lab Nascent Pipeline.
• nf-core Nascent: nascent transcription processing pipeline built using Nextflow.
• NRSA: analyze nascent transcription profiles generated by PRO-seq and GRO-seq data. NRSA quantifies nascent transcription for known genes, and detects, annotates, and quantifies active enhancers. NRSA predicts enhancer targets based on the closest TSS and/or using enhancer-TSS associations from FANTOM5 and 4DGenome where available.
• PEPPRO: a pipeline for PRO-seq, GRO-seq, and ChRO-seq data that 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.
• Proseq2.0: Preprocesses and aligns run-on sequencing (PRO/GRO/ChRO-seq) data from Single-Read or Paired-End Illumina Sequencing.

Read quantification

• DENR: performs annotation based transcript level quantification on nascent RNA sequencing data. Explains observed polymerase density as a weighted mixture of the underlying transcript annotations.

Region based annotations

• FStitch: Fast Stitch Reader (FStitch) rapidly processes read coverage files into contigs of active and inactive regions of transcription. Intended for refining annotations in nascent transcription data.
• Tfit: Annotate sites of bidirectional transcription

Identifying regulatory elements

• dReg: Detection of Regulatory DNA Sequences using GRO-seq Data.

Differential analyses

• tfTarget: identify differentially regulated TF networks based on comparative conditions (e.g. Treatment -vs- Control).

Simulating nascent sequencing

• nascentRNASim: simulate nascent RNA-seq based on empirical data.

Guides and walkthroughs

• GRO-seq guide: GRO-seq analysis guide with HOMER.