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TopHat-Recondition: a post-processor for TopHat unmapped reads

BACKGROUND: TopHat is a popular spliced junction mapper for RNA sequencing data, and writes files in the BAM format – the binary version of the Sequence Alignment/Map (SAM) format. BAM is the standard exchange format for aligned sequencing reads, thus correct format implementation is paramount for s...

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Detalles Bibliográficos
Autores principales: Brueffer, Christian, Saal, Lao H.
Formato: Online Artículo Texto
Lenguaje:English
Publicado: BioMed Central 2016
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4855331/
https://www.ncbi.nlm.nih.gov/pubmed/27142976
http://dx.doi.org/10.1186/s12859-016-1058-x
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author Brueffer, Christian
Saal, Lao H.
author_facet Brueffer, Christian
Saal, Lao H.
author_sort Brueffer, Christian
collection PubMed
description BACKGROUND: TopHat is a popular spliced junction mapper for RNA sequencing data, and writes files in the BAM format – the binary version of the Sequence Alignment/Map (SAM) format. BAM is the standard exchange format for aligned sequencing reads, thus correct format implementation is paramount for software interoperability and correct analysis. However, TopHat writes its unmapped reads in a way that is not compatible with other software that implements the SAM/BAM format. RESULTS: We have developed TopHat-Recondition, a post-processor for TopHat unmapped reads that restores read information in the proper format. TopHat-Recondition thus enables downstream software to process the plethora of BAM files written by TopHat. CONCLUSIONS: TopHat-Recondition can repair unmapped read files written by TopHat and is freely available under a 2-clause BSD license on GitHub: https://github.com/cbrueffer/tophat-recondition. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (doi:10.1186/s12859-016-1058-x) contains supplementary material, which is available to authorized users.
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spelling pubmed-48553312016-05-16 TopHat-Recondition: a post-processor for TopHat unmapped reads Brueffer, Christian Saal, Lao H. BMC Bioinformatics Software BACKGROUND: TopHat is a popular spliced junction mapper for RNA sequencing data, and writes files in the BAM format – the binary version of the Sequence Alignment/Map (SAM) format. BAM is the standard exchange format for aligned sequencing reads, thus correct format implementation is paramount for software interoperability and correct analysis. However, TopHat writes its unmapped reads in a way that is not compatible with other software that implements the SAM/BAM format. RESULTS: We have developed TopHat-Recondition, a post-processor for TopHat unmapped reads that restores read information in the proper format. TopHat-Recondition thus enables downstream software to process the plethora of BAM files written by TopHat. CONCLUSIONS: TopHat-Recondition can repair unmapped read files written by TopHat and is freely available under a 2-clause BSD license on GitHub: https://github.com/cbrueffer/tophat-recondition. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (doi:10.1186/s12859-016-1058-x) contains supplementary material, which is available to authorized users. BioMed Central 2016-05-04 /pmc/articles/PMC4855331/ /pubmed/27142976 http://dx.doi.org/10.1186/s12859-016-1058-x Text en © Brueffer and Saal. 2016 Open Access This article is distributed under the terms of the Creative Commons Attribution 4.0 International License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted use, distribution, and reproduction in any medium, provided you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated.
spellingShingle Software
Brueffer, Christian
Saal, Lao H.
TopHat-Recondition: a post-processor for TopHat unmapped reads
title TopHat-Recondition: a post-processor for TopHat unmapped reads
title_full TopHat-Recondition: a post-processor for TopHat unmapped reads
title_fullStr TopHat-Recondition: a post-processor for TopHat unmapped reads
title_full_unstemmed TopHat-Recondition: a post-processor for TopHat unmapped reads
title_short TopHat-Recondition: a post-processor for TopHat unmapped reads
title_sort tophat-recondition: a post-processor for tophat unmapped reads
topic Software
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4855331/
https://www.ncbi.nlm.nih.gov/pubmed/27142976
http://dx.doi.org/10.1186/s12859-016-1058-x
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