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Terminus enables the discovery of data-driven, robust transcript groups from RNA-seq data
MOTIVATION: Advances in sequencing technology, inference algorithms and differential testing methodology have enabled transcript-level analysis of RNA-seq data. Yet, the inherent inferential uncertainty in transcript-level abundance estimation, even among the most accurate approaches, means that rob...
Autores principales: | , , , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
Oxford University Press
2020
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7355257/ https://www.ncbi.nlm.nih.gov/pubmed/32657377 http://dx.doi.org/10.1093/bioinformatics/btaa448 |
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author | Sarkar, Hirak Srivastava, Avi Bravo, Héctor Corrada Love, Michael I Patro, Rob |
author_facet | Sarkar, Hirak Srivastava, Avi Bravo, Héctor Corrada Love, Michael I Patro, Rob |
author_sort | Sarkar, Hirak |
collection | PubMed |
description | MOTIVATION: Advances in sequencing technology, inference algorithms and differential testing methodology have enabled transcript-level analysis of RNA-seq data. Yet, the inherent inferential uncertainty in transcript-level abundance estimation, even among the most accurate approaches, means that robust transcript-level analysis often remains a challenge. Conversely, gene-level analysis remains a common and robust approach for understanding RNA-seq data, but it coarsens the resulting analysis to the level of genes, even if the data strongly support specific transcript-level effects. RESULTS: We introduce a new data-driven approach for grouping together transcripts in an experiment based on their inferential uncertainty. Transcripts that share large numbers of ambiguously-mapping fragments with other transcripts, in complex patterns, often cannot have their abundances confidently estimated. Yet, the total transcriptional output of that group of transcripts will have greatly reduced inferential uncertainty, thus allowing more robust and confident downstream analysis. Our approach, implemented in the tool terminus, groups together transcripts in a data-driven manner allowing transcript-level analysis where it can be confidently supported, and deriving transcriptional groups where the inferential uncertainty is too high to support a transcript-level result. AVAILABILITY AND IMPLEMENTATION: Terminus is implemented in Rust, and is freely available and open source. It can be obtained from https://github.com/COMBINE-lab/Terminus. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online. |
format | Online Article Text |
id | pubmed-7355257 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2020 |
publisher | Oxford University Press |
record_format | MEDLINE/PubMed |
spelling | pubmed-73552572020-07-16 Terminus enables the discovery of data-driven, robust transcript groups from RNA-seq data Sarkar, Hirak Srivastava, Avi Bravo, Héctor Corrada Love, Michael I Patro, Rob Bioinformatics Comparative and Functional Genomics MOTIVATION: Advances in sequencing technology, inference algorithms and differential testing methodology have enabled transcript-level analysis of RNA-seq data. Yet, the inherent inferential uncertainty in transcript-level abundance estimation, even among the most accurate approaches, means that robust transcript-level analysis often remains a challenge. Conversely, gene-level analysis remains a common and robust approach for understanding RNA-seq data, but it coarsens the resulting analysis to the level of genes, even if the data strongly support specific transcript-level effects. RESULTS: We introduce a new data-driven approach for grouping together transcripts in an experiment based on their inferential uncertainty. Transcripts that share large numbers of ambiguously-mapping fragments with other transcripts, in complex patterns, often cannot have their abundances confidently estimated. Yet, the total transcriptional output of that group of transcripts will have greatly reduced inferential uncertainty, thus allowing more robust and confident downstream analysis. Our approach, implemented in the tool terminus, groups together transcripts in a data-driven manner allowing transcript-level analysis where it can be confidently supported, and deriving transcriptional groups where the inferential uncertainty is too high to support a transcript-level result. AVAILABILITY AND IMPLEMENTATION: Terminus is implemented in Rust, and is freely available and open source. It can be obtained from https://github.com/COMBINE-lab/Terminus. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online. Oxford University Press 2020-07 2020-07-13 /pmc/articles/PMC7355257/ /pubmed/32657377 http://dx.doi.org/10.1093/bioinformatics/btaa448 Text en © The Author(s) 2020. Published by Oxford University Press. http://creativecommons.org/licenses/by-nc/4.0/ This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/4.0/), which permits non-commercial re-use, distribution, and reproduction in any medium, provided the original work is properly cited. For commercial re-use, please contact journals.permissions@oup.com |
spellingShingle | Comparative and Functional Genomics Sarkar, Hirak Srivastava, Avi Bravo, Héctor Corrada Love, Michael I Patro, Rob Terminus enables the discovery of data-driven, robust transcript groups from RNA-seq data |
title | Terminus enables the discovery of data-driven, robust transcript groups from RNA-seq data |
title_full | Terminus enables the discovery of data-driven, robust transcript groups from RNA-seq data |
title_fullStr | Terminus enables the discovery of data-driven, robust transcript groups from RNA-seq data |
title_full_unstemmed | Terminus enables the discovery of data-driven, robust transcript groups from RNA-seq data |
title_short | Terminus enables the discovery of data-driven, robust transcript groups from RNA-seq data |
title_sort | terminus enables the discovery of data-driven, robust transcript groups from rna-seq data |
topic | Comparative and Functional Genomics |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7355257/ https://www.ncbi.nlm.nih.gov/pubmed/32657377 http://dx.doi.org/10.1093/bioinformatics/btaa448 |
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