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          Institute: MPI für molekulare Genetik     Collection: Sequencing Group     Display Documents



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ID: 416181.0, MPI für molekulare Genetik / Sequencing Group
Bisulfite sequencing Data Presentation and Compilation (BDPC) web server--a useful tool for DNA methylation analysis
Authors:Rohde, Christian; Zhang, Yingying; Jurkowski, Tomasz P.; Stamerjohanns, Heinrich; Reinhardt, Richard; Jeltsch, Albert
Language:English
Research Context:Methods Online
Date of Publication (YYYY-MM-DD):2008-02-22
Title of Journal:Nucleic Acids Research
Journal Abbrev.:Nucleic Acids Res
Volume:36
Issue / Number:5
Start Page:e34
End Page:e34
Copyright:© 2008 The Author(s)
This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/2.0/uk/) which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.
Review Status:not specified
Audience:Experts Only
Abstract / Description:During bisulfite genomic sequencing projects large amount of data are generated. The Bisulfite sequencing Data Presentation and Compilation (BDPC) web interface (http://biochem.jacobs-university.de/BDPC/) automatically analyzes bisulfite datasets prepared using the BiQ Analyzer. BDPC provides the following output: (i) MS-Excel compatible files compiling for each PCR product (a) the average methylation level, the number of clones analyzed and the percentage of CG sites analyzed (which is an indicator of data quality), (b) the methylation level observed at each CG site and (c) the methylation level of each clone. (ii) A methylation overview table compiling the methylation of all amplicons in all tissues. (iii) Publication grade figures in PNG format showing the methylation pattern for each PCR product embedded in an HMTL file summarizing the methylation data, the DNA sequence and some basic statistics. (iv) A summary file compiling the methylation pattern of different tissues, which is linked to the individual HTML result files, and can be directly used for presentation of the data in the internet. (v) A condensed file, containing all primary data in simplified format for further downstream data analysis and (vi) a custom track file for display of the results in the UCSC genome browser.
Comment of the Author/Creator:To whom correspondence should be addressed:
Tel: +49 421 200 3247; Fax: +49 421 200 3249;
Email: a.jeltsch@jacobs-university.de
External Publication Status:published
Document Type:Article
Communicated by:Richard Reinhardt
Affiliations:MPI für molekulare Genetik
External Affiliations:1.School of Engineering and Science, Jacobs University Bremen, Campus Ring 1, 28725 Bremen, Germany.
Identifiers:URL:http://nar.oxfordjournals.org/cgi/reprint/36/5/e34
DOI:10.1093/nar/gkn083
ISSN:0305-1048
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