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dc.contributor.authorKrause, Maximilian
dc.contributor.authorNiazi, Adnan Muhammad
dc.contributor.authorLabun, Kornel
dc.contributor.authorTorres Cleuren, Yamila Nicole
dc.contributor.authorMüller, Florian S
dc.contributor.authorValen, Eivind
dc.PublishedKrause 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;25:1229-1241eng
dc.description.abstractPolyadenylation 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.publisherCold Spring Harbor Laboratory Pressen_US
dc.rightsAttribution CC BYeng
dc.subjectpoly(A) taileng
dc.subjectnanopore sequencingeng
dc.subjectR packageeng
dc.titleTailFindR: Alignment-free poly(A) length measurement for Oxford Nanopore RNA and DNA sequencingen_US
dc.typePeer reviewed
dc.typeJournal article
dc.rights.holderCopyright 2019 The Author(s)en_US
dc.source.journalRNA: A publication of the RNA Society

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