TY - JOUR T1 - A technology-agnostic long-read analysis pipeline for transcriptome discovery and quantification JF - bioRxiv DO - 10.1101/672931 SP - 672931 AU - Dana Wyman AU - Gabriela Balderrama-Gutierrez AU - Fairlie Reese AU - Shan Jiang AU - Sorena Rahmanian AU - Weihua Zeng AU - Brian Williams AU - Diane Trout AU - Whitney England AU - Sophie Chu AU - Robert C. Spitale AU - Andrea Tenner AU - Barbara Wold AU - Ali Mortazavi Y1 - 2019/01/01 UR - http://biorxiv.org/content/early/2019/06/18/672931.abstract N2 - Alternative splicing is widely acknowledged to be a crucial regulator of gene expression and is a key contributor to both normal developmental processes and disease states. While cost-effective and accurate for quantification, short-read RNA-seq lacks the ability to resolve full-length transcript isoforms despite increasingly sophisticated computational methods. Long-read sequencing platforms such as Pacific Biosciences (PacBio) and Oxford Nanopore (ONT) bypass the transcript reconstruction challenges of short-reads. Here we describe TALON, the ENCODE4 pipeline for analyzing PacBio cDNA and ONT direct-RNA transcriptomes. We apply TALON to three human ENCODE Tier 1 cell lines and show that while both technologies perform well at full-transcript discovery and quantification, each technology has its distinct artifacts. We further apply TALON to mouse cortical and hippocampal transcriptomes and find that a substantial proportion of neuronal genes have more reads associated with novel isoforms than annotated ones. The TALON pipeline for technology-agnostic, long-read transcriptome discovery and quantification tracks both known and novel transcript models as well as expression levels across datasets for both simple studies and larger projects such as ENCODE that seek to decode transcriptional regulation in the human and mouse genomes to predict more accurate expression levels of genes and transcripts than possible with short-reads alone. ER -