Epigenomic, Bioinformatics, Software, Transcriptomic
Date: July 29, 2025, Action: Dataset publish
Data Type: Readme, File Attributes: MD5 checksum: 450ef019cf8ba58beb644ef18d1411d0
This dataset contains too many files that are not individually described
Data Type: Tabular data, File Attributes: MD5 checksum: 97ee210d263c783e4ddfe20352831d60 Figure in MS: 3
Data Type: GitHub archive, File Attributes: MD5 checksum: 4b4d2ce7259e5045d89b731b7bfcf730 SWH: swh:1:snp:ee789638699e0e33ca3b1d09da5bb1f485ea7c70 license: MPL 2.0
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Archival copy of the GitHub repository https://github.com/haotianteng/BoostNano downloaded 18-July-2025. BoostNano, a tool for preprocessing ONT-Nanopore RNA sequencing reads.This project is licensed under the MPL 2.0 license. Please refer to the GitHub repo for most recent updates.
National Health and Medical Research Council
PolyA tail lengths as found by Boostnano for R1 sequins which were filtered out by Dorado but kept by Boostnano; underlying data for figure 3
Polyadenylation is a dynamic process which is important in cellular physiology. Oxford Nanopore Technologies direct RNA-sequencing provides a strategy for sequencing the full-length RNA molecule and analysis of the transcriptome and epi-transcriptome. There are currently several tools available for poly(A) tail-length estimation, including well-established tools such as tailfindr and nanopolish, as well as two more recent deep learning models: Dorado and BoostNano. However, there has been limited benchmarking of the accuracy of these tools against gold-standard datasets. In this paper we evaluate four poly(A) estimation tools using synthetic RNA standards (Sequins), which have known poly(A) tail-lengths and provide a valuable approach to measuring the accuracy of poly(A) tail-length estimation. All four tools generate mean tail-length estimates which lie within 12% of the correct value. Overall, Dorado is recommended as the preferred approach due to its relatively fast run times, low coefficient of variation and ease of use with integration with base-calling.
oxford nanopore technologies, poly(a) tail, estimation, segmentation, direct rna sequencing
Supporting data for "Using synthetic RNA to benchmark poly(A) length inference from direct RNA sequencing."
Chang JJ, Coin LJM, Teng H, Corbin V, Yang X, and Reames B. "Supporting data for "Using synthetic RNA to benchmark poly(A) length inference from direct RNA sequencing."." ROHub. Jul 29 ,2025. https://w3id.org/ro-id/3543b082-9077-492e-a4c7-a3b7c8bb39e8.
Oxford Nanopore Technologies direct RNA-sequencing provides a strategy for sequencing the full-length RNA molecule and analysis of the transcriptome and epi-transcriptome.
Economy, business and finance/Economic sector/Process industry/Textile and clothing
In this paper we evaluate four poly(A) estimation tools using synthetic RNA standards (Sequins), which have known poly(A) tail-lengths and provide a valuable approach to measuring the accuracy of poly(A) tail-length estimation.
Science and technology/Natural science/Biology/Genetics
Supporting data for "Using synthetic RNA to benchmark poly(A) length inference from direct RNA sequencing.