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Swimming downstream: statistical analysis of differential transcript usage following Salmon quantification
Detection of differential transcript usage (DTU) from RNA-seq data is an important bioinformatic analysis that complements differential gene expression analysis. Here we present a simple workflow using a set of existing R/Bioconductor packages for analysis of DTU. We show how these packages can be u...
Autores principales: | , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
F1000 Research Limited
2018
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6178912/ https://www.ncbi.nlm.nih.gov/pubmed/30356428 http://dx.doi.org/10.12688/f1000research.15398.3 |
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author | Love, Michael I. Soneson, Charlotte Patro, Rob |
author_facet | Love, Michael I. Soneson, Charlotte Patro, Rob |
author_sort | Love, Michael I. |
collection | PubMed |
description | Detection of differential transcript usage (DTU) from RNA-seq data is an important bioinformatic analysis that complements differential gene expression analysis. Here we present a simple workflow using a set of existing R/Bioconductor packages for analysis of DTU. We show how these packages can be used downstream of RNA-seq quantification using the Salmon software package. The entire pipeline is fast, benefiting from inference steps by Salmon to quantify expression at the transcript level. The workflow includes live, runnable code chunks for analysis using DRIMSeq and DEXSeq, as well as for performing two-stage testing of DTU using the stageR package, a statistical framework to screen at the gene level and then confirm which transcripts within the significant genes show evidence of DTU. We evaluate these packages and other related packages on a simulated dataset with parameters estimated from real data. |
format | Online Article Text |
id | pubmed-6178912 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2018 |
publisher | F1000 Research Limited |
record_format | MEDLINE/PubMed |
spelling | pubmed-61789122018-10-22 Swimming downstream: statistical analysis of differential transcript usage following Salmon quantification Love, Michael I. Soneson, Charlotte Patro, Rob F1000Res Method Article Detection of differential transcript usage (DTU) from RNA-seq data is an important bioinformatic analysis that complements differential gene expression analysis. Here we present a simple workflow using a set of existing R/Bioconductor packages for analysis of DTU. We show how these packages can be used downstream of RNA-seq quantification using the Salmon software package. The entire pipeline is fast, benefiting from inference steps by Salmon to quantify expression at the transcript level. The workflow includes live, runnable code chunks for analysis using DRIMSeq and DEXSeq, as well as for performing two-stage testing of DTU using the stageR package, a statistical framework to screen at the gene level and then confirm which transcripts within the significant genes show evidence of DTU. We evaluate these packages and other related packages on a simulated dataset with parameters estimated from real data. F1000 Research Limited 2018-10-01 /pmc/articles/PMC6178912/ /pubmed/30356428 http://dx.doi.org/10.12688/f1000research.15398.3 Text en Copyright: © 2018 Love MI et al. http://creativecommons.org/licenses/by/4.0/ This is an open access article distributed under the terms of the Creative Commons Attribution Licence, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. |
spellingShingle | Method Article Love, Michael I. Soneson, Charlotte Patro, Rob Swimming downstream: statistical analysis of differential transcript usage following Salmon quantification |
title | Swimming downstream: statistical analysis of differential transcript usage following Salmon quantification |
title_full | Swimming downstream: statistical analysis of differential transcript usage following Salmon quantification |
title_fullStr | Swimming downstream: statistical analysis of differential transcript usage following Salmon quantification |
title_full_unstemmed | Swimming downstream: statistical analysis of differential transcript usage following Salmon quantification |
title_short | Swimming downstream: statistical analysis of differential transcript usage following Salmon quantification |
title_sort | swimming downstream: statistical analysis of differential transcript usage following salmon quantification |
topic | Method Article |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6178912/ https://www.ncbi.nlm.nih.gov/pubmed/30356428 http://dx.doi.org/10.12688/f1000research.15398.3 |
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