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BISMA - Fast and accurate bisulfite sequencing data analysis of individual clones from unique and repetitive sequences

Christian Rohde1, Yingying Zhang1, Richard Reinhardt2 and Albert Jeltsch1*

Author Affiliations

1 School of Engineering and Science, Jacobs University Bremen, Campus Ring 1, 28725 Bremen, Germany

2 Max Planck Institute for Molecular Genetics, Ihnestrasse 63-73, D-14195 Berlin-Dahlem, Germany

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BMC Bioinformatics 2010, 11:230  doi:10.1186/1471-2105-11-230

Published: 6 May 2010

Additional files

Additional file 1:

Supplemental Text S1. Correlation between number of analyzed clones and precision of the estimate of biological methylation levels. Supplemental Text S2. Examples in literature for bisulfite sequencing of subcloned PCR-products obtained from repetitive elements. Supplemental Text S3. Improved CpG site detection and improved annotation of the methylation state. Supplemental Text S4. Improved CpG site detection. Supplemental Text S5. Improved annotation of the methylation state. Supplemental Text S6. Automatic detection of clonal molecules. Supplemental Text S7. Improved detection of clonal molecules avoids inappropriate filtering of valid sequences. Supplemental Text S8. Improved detection of clonal molecules ignores N-sites at cytosine positions. Supplemental Figure S9. Complete alignment of all bisulfite sequencing data used to create the results shown in Figure 3C.

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