Figure 2

Design and implementation of the ngs.plot program. A. In RNA-seq mode, the program performs exon splicing in silico: the coverage vectors for exons are concatenated with intronic coverage removed. B. A configuration file can be used to create any combination of BAM files and regions. The program will parse the configuration and perform pre-processing on BAM files. It will then iterate through each line of the configuration and determine the arrangement of the output figure. C. A genome crawler is developed to automatically pull genomic annotations from three public databases – UCSC genome browser, Ensembl and ENCODE. It then performs more elaborate classifications on the functional elements and compiles them into R binary tables. D. The exon classification algorithm classifies exons into seven categories: promoter, variant, alternative donor, alternative acceptor, alternative both, and polyA based on pairwise comparisons of exon boundaries.