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Error correction in methylation profiling from NGS bisulfite protocols. (English) Zbl 07229386
Elloumi, Mourad (ed.), Algorithms for next-generation sequencing data. Techniques, approaches, and applications. Cham: Springer (ISBN 978-3-319-59824-6/hbk; 978-3-319-59826-0/ebook). 167-183 (2017).
Summary: Whole genome bisulfite sequencing (WGBS) has emerged as the primary technique for DNA methylation studies, because of its great potential in terms of speed, specificity, and the capability of addressing new biological implications as non-CpG context methylation or hemimethylation. However, despite the improvement that has meant the appearance of WGBS, processing and analyzing the resulting datasets is not as straightforward as in other methylation assays, and special care should be taken to obtain reliable results. As far as we know, an extensive review on the error sources that can bias methylation level measurement and the different algorithms that have been proposed to deal with it does not exist. Therefore, in this chapter all known WGBS error sources will be extensively reviewed and critically evaluated in order to suggest a couple of best practices to deal with all sources of bias in WGBS assays.
For the entire collection see [Zbl 1383.68005].
MSC:
68W32 Algorithms on strings
92D20 Protein sequences, DNA sequences
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