Using Nanopore Sequencing to Interrogate the Genome and Epigenome

This work involves using native RNA nanopore sequencing to directly characterize the transcriptome of a human cell line, GM12878. We demonstrated several new methods, and findings, including newly discovered isoforms, allele-specific isoforms, measurement of polyadenylation length, and even measurement of RNA modifications. We also describe an application of nanopore RNA sequencing and chemical labeling to measure the secondary structure of RNA. Lastly, we demonstrate an analysis framework for looking at a new file format for single-molecule/long-read modification data