TailFindR: Alignment-free poly(A) length measurement for Oxford Nanopore RNA and DNA sequencing
Peer reviewed, Journal article
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Original versionKrause 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 https://doi.org/10.1261/rna.071332.119
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.