tailfindr : alignment-free poly(A) length measurement for Oxford Nanopore RNA and DNA sequencing.

Autor:	Krause M; Computational Biology Unit, Department of Informatics, University of Bergen, 5008 Bergen, Norway.; Sars International Centre for Marine Molecular Biology, University of Bergen, 5008 Bergen, Norway., Niazi AM; Computational Biology Unit, Department of Informatics, University of Bergen, 5008 Bergen, Norway., Labun K; Computational Biology Unit, Department of Informatics, University of Bergen, 5008 Bergen, Norway., Torres Cleuren YN; Computational Biology Unit, Department of Informatics, University of Bergen, 5008 Bergen, Norway., Müller FS; Computational Biology Unit, Department of Informatics, University of Bergen, 5008 Bergen, Norway., Valen E; Computational Biology Unit, Department of Informatics, University of Bergen, 5008 Bergen, Norway.; Sars International Centre for Marine Molecular Biology, University of Bergen, 5008 Bergen, Norway.
Jazyk:	angličtina
Zdroj:	RNA (New York, N.Y.) [RNA] 2019 Oct; Vol. 25 (10), pp. 1229-1241. Date of Electronic Publication: 2019 Jul 02.
DOI:	10.1261/rna.071332.119
Abstrakt:	Polyadenylation at the 3'-end is a major regulator of messenger RNA and its length is known to affect nuclear export, stability, and translation, among others. Only recently have strategies emerged that allow for genome-wide poly(A) length assessment. These methods identify genes connected to poly(A) tail measurements indirectly by short-read alignment to genetic 3'-ends. Concurrently, Oxford Nanopore Technologies (ONT) established full-length isoform-specific RNA sequencing containing the entire poly(A) tail. However, assessing poly(A) length through base-calling has so far not been possible due to the inability to resolve long homopolymeric stretches in ONT sequencing. Here we present tailfindr , an R package to estimate poly(A) tail length on ONT long-read sequencing data. tailfindr operates on unaligned, base-called data. It measures poly(A) tail length from both native RNA and DNA sequencing, which makes poly(A) tail studies by full-length cDNA approaches possible for the first time. We assess tailfindr 's performance across different poly(A) lengths, demonstrating that tailfindr is a versatile tool providing poly(A) tail estimates across a wide range of sequencing conditions. (© 2019 Krause et al.; Published by Cold Spring Harbor Laboratory Press for the RNA Society.)
Databáze:	MEDLINE
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