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

Maximilian Krause, View ORCID ProfileAdnan M. Niazi, View ORCID ProfileKornel Labun, View ORCID ProfileYamila N. Torres Cleuren, View ORCID ProfileFlorian S. Müller, View ORCID ProfileEivind Valen
doi: https://doi.org/10.1101/588343
Maximilian Krause
1Computational Biology Unit, Department of Informatics, University of Bergen, 5008 Bergen, Norway
2Sars International Centre for Marine Molecular Biology, University of Bergen, 5008 Bergen, Norway
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Adnan M. Niazi
1Computational Biology Unit, Department of Informatics, University of Bergen, 5008 Bergen, Norway
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Kornel Labun
1Computational Biology Unit, Department of Informatics, University of Bergen, 5008 Bergen, Norway
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Yamila N. Torres Cleuren
1Computational Biology Unit, Department of Informatics, University of Bergen, 5008 Bergen, Norway
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Florian S. Müller
1Computational Biology Unit, Department of Informatics, University of Bergen, 5008 Bergen, Norway
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Eivind Valen
1Computational Biology Unit, Department of Informatics, University of Bergen, 5008 Bergen, Norway
2Sars International Centre for Marine Molecular Biology, University of Bergen, 5008 Bergen, Norway
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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, strategies have 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 RNA sequencing containing the entire poly(A) tail. However, assessing poly(A) length through basecalling has so far not been possible due 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, basecalled 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.

Footnotes

  • Code Repository: https://github.com/adnaniazi/tailfindr

Copyright 
The copyright holder for this preprint is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under a CC-BY-NC-ND 4.0 International license.
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Posted March 26, 2019.
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tailfindr: Alignment-free poly(A) length measurement for Oxford Nanopore RNA and DNA sequencing
Maximilian Krause, Adnan M. Niazi, Kornel Labun, Yamila N. Torres Cleuren, Florian S. Müller, Eivind Valen
bioRxiv 588343; doi: https://doi.org/10.1101/588343
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tailfindr: Alignment-free poly(A) length measurement for Oxford Nanopore RNA and DNA sequencing
Maximilian Krause, Adnan M. Niazi, Kornel Labun, Yamila N. Torres Cleuren, Florian S. Müller, Eivind Valen
bioRxiv 588343; doi: https://doi.org/10.1101/588343

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