The nASAP (nAScent RNA data Analysis Platform) is dedicated to providing quality assessment and comprehensive interpretation of nascent RNA profiling datasets (e.g., GRO-seq, PRO-seq, NET-seq and TT-seq). The main 4 modules including in this tool are Summarized below:
1. Systematic Quality Assessment. For any dataset pre-processed by nASAP or submitted by users, nASAP will return a web-based report to summarize the sequencing statistics, mapping ratio, RNA integrity, mRNA contamination, and run-on efficiency.
2. Transcription Level Quantification. Transcription levels will be quantified for protein-coding genes, lncRNAs and eRNAs. Advanced options are available, e.g., differential gene expression analysis if nascent RNA profiling data in two conditions are provided.
3. Pausing Index Calculation and Pausing Site Identification. Promoter-proximal pausing indexes are calculated for individual genes, and compared with other nASAP datasets to define cell-type specific pausing. Pausing sites other than promoter-proximal regions are also deduced based on the distribution of nascent RNA across the gene bodies.
4. Regulatory Network Construction.Active enhancers with eRNA signatures will be identified. Moreover, nASAP will tentatively deduce the enhancer-promoter interactomes for better understanding the gene regulatory network.
The following figure summarizes the main functions of nASAP.
