BAT: Bisulfite Analysis Toolkit: BAT is a toolkit to analyze DNA methylation sequencing data accurately and reproducibly. It covers standard processing and analysis steps from raw read mapping up to annotation data integration and calculation of correlating DMRs.

Here, we present BAT, a modular bisulfite analysis toolkit, that facilitates the analysis of bisulfite sequencing data. It covers the essential analysis steps of read alignment, quality control, extraction of methylation information, and calling of differentially methylated regions, as well as biolo...

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Detalles Bibliográficos
Autores principales: Kretzmer, Helene, Otto, Christian, Hoffmann, Steve
Formato: Online Artículo Texto
Lenguaje:English
Publicado: F1000Research 2017
Materias:
Software Tool Article
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5590080/
https://www.ncbi.nlm.nih.gov/pubmed/28979767
http://dx.doi.org/10.12688/f1000research.12302.1
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author Kretzmer, Helene
Otto, Christian
Hoffmann, Steve
author_facet Kretzmer, Helene
Otto, Christian
Hoffmann, Steve
author_sort Kretzmer, Helene
collection PubMed
description Here, we present BAT, a modular bisulfite analysis toolkit, that facilitates the analysis of bisulfite sequencing data. It covers the essential analysis steps of read alignment, quality control, extraction of methylation information, and calling of differentially methylated regions, as well as biologically relevant downstream analyses, such as data integration with gene expression, histone modification data, or transcription factor binding site annotation.
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spelling pubmed-55900802017-10-03 BAT: Bisulfite Analysis Toolkit: BAT is a toolkit to analyze DNA methylation sequencing data accurately and reproducibly. It covers standard processing and analysis steps from raw read mapping up to annotation data integration and calculation of correlating DMRs. Kretzmer, Helene Otto, Christian Hoffmann, Steve F1000Res Software Tool Article Here, we present BAT, a modular bisulfite analysis toolkit, that facilitates the analysis of bisulfite sequencing data. It covers the essential analysis steps of read alignment, quality control, extraction of methylation information, and calling of differentially methylated regions, as well as biologically relevant downstream analyses, such as data integration with gene expression, histone modification data, or transcription factor binding site annotation. F1000Research 2017-08-16 /pmc/articles/PMC5590080/ /pubmed/28979767 http://dx.doi.org/10.12688/f1000research.12302.1 Text en Copyright: © 2017 Kretzmer H 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 Software Tool Article
Kretzmer, Helene
Otto, Christian
Hoffmann, Steve
BAT: Bisulfite Analysis Toolkit: BAT is a toolkit to analyze DNA methylation sequencing data accurately and reproducibly. It covers standard processing and analysis steps from raw read mapping up to annotation data integration and calculation of correlating DMRs.
title BAT: Bisulfite Analysis Toolkit: BAT is a toolkit to analyze DNA methylation sequencing data accurately and reproducibly. It covers standard processing and analysis steps from raw read mapping up to annotation data integration and calculation of correlating DMRs.
title_full BAT: Bisulfite Analysis Toolkit: BAT is a toolkit to analyze DNA methylation sequencing data accurately and reproducibly. It covers standard processing and analysis steps from raw read mapping up to annotation data integration and calculation of correlating DMRs.
title_fullStr BAT: Bisulfite Analysis Toolkit: BAT is a toolkit to analyze DNA methylation sequencing data accurately and reproducibly. It covers standard processing and analysis steps from raw read mapping up to annotation data integration and calculation of correlating DMRs.
title_full_unstemmed BAT: Bisulfite Analysis Toolkit: BAT is a toolkit to analyze DNA methylation sequencing data accurately and reproducibly. It covers standard processing and analysis steps from raw read mapping up to annotation data integration and calculation of correlating DMRs.
title_short BAT: Bisulfite Analysis Toolkit: BAT is a toolkit to analyze DNA methylation sequencing data accurately and reproducibly. It covers standard processing and analysis steps from raw read mapping up to annotation data integration and calculation of correlating DMRs.
title_sort bat: bisulfite analysis toolkit: bat is a toolkit to analyze dna methylation sequencing data accurately and reproducibly. it covers standard processing and analysis steps from raw read mapping up to annotation data integration and calculation of correlating dmrs.
topic Software Tool Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5590080/
https://www.ncbi.nlm.nih.gov/pubmed/28979767
http://dx.doi.org/10.12688/f1000research.12302.1
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AT ottochristian batbisulfiteanalysistoolkitbatisatoolkittoanalyzednamethylationsequencingdataaccuratelyandreproduciblyitcoversstandardprocessingandanalysisstepsfromrawreadmappinguptoannotationdataintegrationandcalculationofcorrelatingdmrs
AT hoffmannsteve batbisulfiteanalysistoolkitbatisatoolkittoanalyzednamethylationsequencingdataaccuratelyandreproduciblyitcoversstandardprocessingandanalysisstepsfromrawreadmappinguptoannotationdataintegrationandcalculationofcorrelatingdmrs

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