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Improving RNA-Seq Precision with MapAl
With currently available RNA-Seq pipelines, expression estimates for most genes are very noisy. We here introduce MapAl, a tool for RNA-Seq expression profiling that builds on the established programs Bowtie and Cufflinks. In the post-processing of RNA-Seq reads, it incorporates gene models already...
Autores principales: | , , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
Frontiers Research Foundation
2012
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3316937/ https://www.ncbi.nlm.nih.gov/pubmed/22485116 http://dx.doi.org/10.3389/fgene.2012.00028 |
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author | Łabaj, Paweł P. Linggi, Bryan E. Wiley, H. Steven Kreil, David P. |
author_facet | Łabaj, Paweł P. Linggi, Bryan E. Wiley, H. Steven Kreil, David P. |
author_sort | Łabaj, Paweł P. |
collection | PubMed |
description | With currently available RNA-Seq pipelines, expression estimates for most genes are very noisy. We here introduce MapAl, a tool for RNA-Seq expression profiling that builds on the established programs Bowtie and Cufflinks. In the post-processing of RNA-Seq reads, it incorporates gene models already at the stage of read alignment, increasing the number of reliably measured known transcripts consistently by 50%. Adding genes identified de novo then allows a reliable assessment of double the total number of transcripts compared to other available pipelines. This substantial improvement is of general relevance: Measurement precision determines the power of any analysis to reliably identify significant signals, such as in screens for differential expression, independent of whether the experimental design incorporates replicates or not. |
format | Online Article Text |
id | pubmed-3316937 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2012 |
publisher | Frontiers Research Foundation |
record_format | MEDLINE/PubMed |
spelling | pubmed-33169372012-04-06 Improving RNA-Seq Precision with MapAl Łabaj, Paweł P. Linggi, Bryan E. Wiley, H. Steven Kreil, David P. Front Genet Genetics With currently available RNA-Seq pipelines, expression estimates for most genes are very noisy. We here introduce MapAl, a tool for RNA-Seq expression profiling that builds on the established programs Bowtie and Cufflinks. In the post-processing of RNA-Seq reads, it incorporates gene models already at the stage of read alignment, increasing the number of reliably measured known transcripts consistently by 50%. Adding genes identified de novo then allows a reliable assessment of double the total number of transcripts compared to other available pipelines. This substantial improvement is of general relevance: Measurement precision determines the power of any analysis to reliably identify significant signals, such as in screens for differential expression, independent of whether the experimental design incorporates replicates or not. Frontiers Research Foundation 2012-04-02 /pmc/articles/PMC3316937/ /pubmed/22485116 http://dx.doi.org/10.3389/fgene.2012.00028 Text en Copyright © 2012 Łabaj, Linggi, Wiley and Kreil. http://www.frontiersin.org/licenseagreement This is an open-access article distributed under the terms of the Creative Commons Attribution Non Commercial License, which permits non-commercial use, distribution, and reproduction in other forums, provided the original authors and source are credited. |
spellingShingle | Genetics Łabaj, Paweł P. Linggi, Bryan E. Wiley, H. Steven Kreil, David P. Improving RNA-Seq Precision with MapAl |
title | Improving RNA-Seq Precision with MapAl |
title_full | Improving RNA-Seq Precision with MapAl |
title_fullStr | Improving RNA-Seq Precision with MapAl |
title_full_unstemmed | Improving RNA-Seq Precision with MapAl |
title_short | Improving RNA-Seq Precision with MapAl |
title_sort | improving rna-seq precision with mapal |
topic | Genetics |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3316937/ https://www.ncbi.nlm.nih.gov/pubmed/22485116 http://dx.doi.org/10.3389/fgene.2012.00028 |
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