Abstract
Due to its simple nature, the clustered regularly interspaced short palindromic repeats (CRISPR)—Cas9 technique is massively used nowadays to modify genomic loci in a wide range of model systems. The possibility to interrogate gene function on a genome-wide scale is revolutionizing fundamental life sciences and will lead to new clinical breakthroughs. Its strength is even more pronounced when it is used in tandem with next-generation sequencing (NGS). The high throughput and low cost cause NGS to be the method of choice for exploring CRISPR-Cas9 experimental results. To analyze the NGS reads from genome editing experiments only few bioinformatics tools are available. BATCH-GE is a flexible and easy-to-use tool, which is especially useful for dealing with large amounts of data. It detects and reports indel mutations and other precise genome editing events and calculates the corresponding mutagenesis efficiencies for a large number of samples in parallel.
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References
Boel A, Steyaert W, De Rocker N, Menten B, Callewaert B, De Paepe A, Coucke P, Willaert A (2016) BATCH-GE: Batch analysis of next-generation sequencing data for genome editing assessment. Sci Rep 6:30330. https://doi.org/10.1038/srep30330
Naert T, Colpaert R, Van Nieuwenhuysen T, Dimitrakopoulou D, Leoen J, Haustraete J, Boel A, Steyaert W, Lepez T, Deforce D, Willaert A, Creytens D, Vleminckx K (2016) CRISPR/Cas9 mediated knockout of rb1 and rbl1 leads to rapid and penetrant retinoblastoma development in Xenopus tropicalis. Sci Rep 6:35264. https://doi.org/10.1038/srep35264
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Steyaert, W., Boel, A., Coucke, P., Willaert, A. (2018). BATCH-GE: Analysis of NGS Data for Genome Editing Assessment. In: Vleminckx, K. (eds) Xenopus. Methods in Molecular Biology, vol 1865. Humana Press, New York, NY. https://doi.org/10.1007/978-1-4939-8784-9_6
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DOI: https://doi.org/10.1007/978-1-4939-8784-9_6
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