Journal article

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

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

NAR GENOMICS AND BIOINFORMATICS | OXFORD UNIV PRESS | Published : 2021

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 the high sequence error and small library sizes, which decreases quantification accuracy and reduces power for statistical testing. Here, we report the analysis of two nanopore RNA-seq datasets with the goal of obtaining gene- 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 was analysed using a mix of long-read specific tools for preproces..

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Grants

Awarded by National Health and Medical Research Council (NHMRC)


Awarded by NHMRC Career Development Fellowship


Awarded by NHMRC Early Career Fellowship


Funding Acknowledgements

National Health and Medical Research Council (NHMRC) Project Grant [GNT1098290 to M.E.B., M.E.R.]; NHMRC Career Development Fellowship [GNT1104924 to M.E.R.]; NHMRC Early Career Fellowship [GNT1072662 to M.B.C.]; Bellberry-Viertel Senior Medical Research Fellowship (to M.E.B.); Melbourne Research Scholarship (to X.D., L.T.); Victorian State Government Operational Infrastructure Support and Australian Government NHMRC IRIISS.