dc.contributor.author | Krause, Maximilian | |
dc.contributor.author | Niazi, Adnan Muhammad | |
dc.contributor.author | Labun, Kornel | |
dc.contributor.author | Torres Cleuren, Yamila Nicole | |
dc.contributor.author | Müller, Florian S | |
dc.contributor.author | Valen, Eivind | |
dc.date.accessioned | 2020-05-29T16:34:28Z | |
dc.date.available | 2020-05-29T16:34:28Z | |
dc.date.issued | 2019-07-02 | |
dc.Published | Krause M, Niazi AM, Labun K, Torres Cleuren YN, Müller, Valen E. TailFindR: Alignment-free poly(A) length measurement for Oxford Nanopore RNA and DNA sequencing. RNA: A publication of the RNA Society. 2019;25:1229-1241 | eng |
dc.identifier.issn | 1355-8382 | en_US |
dc.identifier.issn | 1469-9001 | en_US |
dc.identifier.uri | https://hdl.handle.net/1956/22421 | |
dc.description.abstract | 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. | en_US |
dc.language.iso | eng | eng |
dc.publisher | Cold Spring Harbor Laboratory Press | en_US |
dc.rights | Attribution CC BY | eng |
dc.rights.uri | http://creativecommons.org/licenses/by/4.0/ | eng |
dc.subject | poly(A) tail | eng |
dc.subject | nanopore sequencing | eng |
dc.subject | cDNA | eng |
dc.subject | R package | eng |
dc.title | TailFindR: Alignment-free poly(A) length measurement for Oxford Nanopore RNA and DNA sequencing | en_US |
dc.type | Peer reviewed | |
dc.type | Journal article | |
dc.date.updated | 2020-01-10T12:47:20Z | |
dc.description.version | publishedVersion | en_US |
dc.rights.holder | Copyright 2019 The Author(s) | en_US |
dc.identifier.doi | https://doi.org/10.1261/rna.071332.119 | |
dc.identifier.cristin | 1742204 | |
dc.source.journal | RNA: A publication of the RNA Society | |