A technology-agnostic long-read analysis pipeline for transcriptome discovery and quantification
Year: 2019
Type: other
Abstract: Conventional short-read RNA sequencing has been widely used to quantify gene expression in a variety of applications. However, short reads on their own lack the ability to resolve full-length isoforms, which can be several kilobases in length. While long read technologies such as PacBio cDNA sequencing and Oxford Nanopore direct RNA sequencing have a higher error rate than short reads, they hold great potential for isoform discovery and characterization of the 90% of multi-exon human genes that are thought to undergo alternative splicing. We have developed TALON, a computational pipeline to process long reads into cleaned isoforms and to compare them to existing annotations. TALON tracks isoforms and expression levels across different datasets as well as sequencing platforms, allowing novel discoveries to be vetted and quantified. We demonstrate our pipeline on PacBio and Oxford Nanopore transcriptomes from both human and mouse ENCODE samples. We also extend the TALON methodology to single cells from the developing mouse limb bud sequenced using the PacBio Sequel2 platform. By comparing our results to existing FANTOM and ENCODE consortium data, we show that long read technologies are mature enough to quantify and characterize full-length transcriptomes.
Institution: University of California, Irvine
Language: English
Subfield: Molecular Biology
Domain: Life Sciences
Open Access status: gold
OpenAlex ID: W3081893569