Partitioning RNAs by length improves transcriptome reconstruction from short-read RNA-seq data-Reference-Cited by-同舟云学术

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Partitioning RNAs by length improves transcriptome reconstruction from short-read RNA-seq data

Published:2022-01-10 Issue:5 Volume:40 Page:741-750
ISSN:1087-0156
Container-title:Nature Biotechnology
language:en
Short-container-title:Nat Biotechnol

Author:

Ringeling Francisca Rojas^ORCID,Chakraborty Shounak,Vissers Caroline,Reiman Derek^ORCID,Patel Akshay M.^ORCID,Lee Ki-Heon,Hong Ari^ORCID,Park Chan-Woo,Reska Tim,Gagneur Julien^ORCID,Chang Hyeshik^ORCID,Spletter Maria L.^ORCID,Yoon Ki-Jun,Ming Guo-li^ORCID,Song Hongjun^ORCID,Canzar Stefan^ORCID

Funder

U.S. Department of Health & Human Services | National Institutes of Health

Simons Foundation

Deutsche Forschungsgemeinschaft

Deutsche Gesellschaft für Muskelkranke

National Research Foundation of Korea

Institute for Basic Science, Korea Suh Kyungbae Foundation, Korea Free State of Bavaria, Germany

Publisher

Springer Science and Business Media LLC

Subject

Biomedical Engineering,Molecular Medicine,Applied Microbiology and Biotechnology,Bioengineering,Biotechnology

Link

https://www.nature.com/articles/s41587-021-01136-7.pdf

Reference68 articles.

1. Zhang, C., Zhang, B., Lin, L.-L. & Zhao, S. Evaluation and comparison of computational tools for RNA-seq isoform quantification. BMC Genomics 18, 583 (2017).

2. Teng, M. et al. A benchmark for RNA-seq quantification pipelines. Genome Biol. 17, 74 (2016).

3. Aguiar, D. et al. Bayesian nonparametric discovery of isoforms and individual specific quantification. Nat. Commun. 9, 1681 (2018).

4. Song, L., Sabunciyan, S., Yang, G. & Florea, L. A multi-sample approach increases the accuracy of transcript assembly. Nat. Commun. 10, 5000 (2019).

5. Li, W. V. et al. AIDE: annotation-assisted isoform discovery with high precision. Genome Res. 29, 2056–2072 (2019).

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