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RNA-Seq Reproducibility Assessment of the Sequencing Quality Control Project
With the widespread RNA-seq applications of different sequencing platforms in biomedical science research in recent years, a systematic evaluation of RNA-seq data quality is crucial and timely. The Sequencing Quality Control (SEQC) project is a large-scale community effort for assessing the performa...
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Formato: | Online Artículo Texto |
Lenguaje: | English |
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SAGE Publications
2020
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Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7241209/ https://www.ncbi.nlm.nih.gov/pubmed/32489246 http://dx.doi.org/10.1177/1176935120922498 |
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author | Yu, Lianbo |
author_facet | Yu, Lianbo |
author_sort | Yu, Lianbo |
collection | PubMed |
description | With the widespread RNA-seq applications of different sequencing platforms in biomedical science research in recent years, a systematic evaluation of RNA-seq data quality is crucial and timely. The Sequencing Quality Control (SEQC) project is a large-scale community effort for assessing the performance of RNA-seq technology across different platforms and multiple laboratories, where reference RNA samples with multiple replicates were sequenced at 12 laboratories using 3 sequencing platforms. Different from the SEQC project, we performed an independent and comprehensive analysis of RNA-seq data of the SEQC project to assess sequencing reproducibility across platforms, sequencing sites, sample replicates, and FlowCells, respectively. With the employment of graphical tools and statistical models, our systemic analysis supports a distinctive conclusion that reproducibility across platforms and sequencing sites are not acceptable, whereas reproducibility across sample replicates and FlowCells are acceptable. |
format | Online Article Text |
id | pubmed-7241209 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2020 |
publisher | SAGE Publications |
record_format | MEDLINE/PubMed |
spelling | pubmed-72412092020-06-01 RNA-Seq Reproducibility Assessment of the Sequencing Quality Control Project Yu, Lianbo Cancer Inform Short Report With the widespread RNA-seq applications of different sequencing platforms in biomedical science research in recent years, a systematic evaluation of RNA-seq data quality is crucial and timely. The Sequencing Quality Control (SEQC) project is a large-scale community effort for assessing the performance of RNA-seq technology across different platforms and multiple laboratories, where reference RNA samples with multiple replicates were sequenced at 12 laboratories using 3 sequencing platforms. Different from the SEQC project, we performed an independent and comprehensive analysis of RNA-seq data of the SEQC project to assess sequencing reproducibility across platforms, sequencing sites, sample replicates, and FlowCells, respectively. With the employment of graphical tools and statistical models, our systemic analysis supports a distinctive conclusion that reproducibility across platforms and sequencing sites are not acceptable, whereas reproducibility across sample replicates and FlowCells are acceptable. SAGE Publications 2020-05-20 /pmc/articles/PMC7241209/ /pubmed/32489246 http://dx.doi.org/10.1177/1176935120922498 Text en © The Author(s) 2020 https://creativecommons.org/licenses/by-nc/4.0/ This article is distributed under the terms of the Creative Commons Attribution-NonCommercial 4.0 License (https://creativecommons.org/licenses/by-nc/4.0/) which permits non-commercial use, reproduction and distribution of the work without further permission provided the original work is attributed as specified on the SAGE and Open Access pages (https://us.sagepub.com/en-us/nam/open-access-at-sage). |
spellingShingle | Short Report Yu, Lianbo RNA-Seq Reproducibility Assessment of the Sequencing Quality Control Project |
title | RNA-Seq Reproducibility Assessment of the Sequencing Quality Control Project |
title_full | RNA-Seq Reproducibility Assessment of the Sequencing Quality Control Project |
title_fullStr | RNA-Seq Reproducibility Assessment of the Sequencing Quality Control Project |
title_full_unstemmed | RNA-Seq Reproducibility Assessment of the Sequencing Quality Control Project |
title_short | RNA-Seq Reproducibility Assessment of the Sequencing Quality Control Project |
title_sort | rna-seq reproducibility assessment of the sequencing quality control project |
topic | Short Report |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7241209/ https://www.ncbi.nlm.nih.gov/pubmed/32489246 http://dx.doi.org/10.1177/1176935120922498 |
work_keys_str_mv | AT yulianbo rnaseqreproducibilityassessmentofthesequencingqualitycontrolproject |