Journal article

The long and the short of it: unlocking nanopore long-read RNA sequencing data with short-read tools

Xueyi Dong, Luyi Tian, Quentin Gouil, Hasaru Kariyawasam, Shian Su, Ricardo De Paoli-Iseppi, Yair David Joseph Prawer, Michael Clark, Kelsey Breslin, Megan Iminitoff, Marnie Blewitt, Charity Law, Matthew Ritchie

Cold Spring Harbor Laboratory | Published : 2020

Abstract

Application of Oxford Nanopore Technologies’ long-read sequencing platform to transcriptomic analysis is increasing in popularity. However, such analysis can be challenging due to small library sizes and high sequence error, which decreases quantification accuracy and reduces power for statistical testing. Here, we report the analysis of two nanopore sequencing RNA-seq datasets with the goal of obtaining gene-level and isoform-level differential expression information. A dataset of synthetic, spliced, spike-in RNAs (“sequins”) as well as a mouse neural stem cell dataset from samples with a null mutation of the epigenetic regulator Smchd1 were analysed using a mix of long-read specific tools ..

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