1B amplified Track Settings
 
Regions amplified in 1B-D1606

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Data schema/format description and download
Assembly: S. cerevisiae Apr. 2011 (SacCer_Apr2011/sacCer3)
Data last updated at UCSC: 2024-03-28 02:38:37

Description

The tracks labeled 'amplified' or 'deleted' contain information about regions which are presumably amplified or deleted Saccharomyces cerevisiae strains of the Peterhof genetic collection. For more information on strains please see the description page.

Methods

Copy number variation was estimated with the mrCaNaVaR pipeline [Alkan et al., 2009]. Subsequent analysis was performed with R. Windows with normalized copy number above 1.8 were considered as amplified while those with copy number below 0.3 were considered as deleted. Windows were merged to calculate length of regions and intersected with reference genome annotation to produce lists of presumably amplified or missing genes.

References

Alkan C, Kidd JM, Marques-Bonet T, Aksay G, Antonacci F, Hormozdiari F, et al. Personalized copy number and segmental duplication maps using next-generation sequencing. Nat Genet [Internet]. Nature Publishing Group; 2009 Oct [cited 2015 Oct 28];41(10):1061–7. Available from: http://www.nature.com/ng/journal/v41/n10/full/ng.437.html

Contacts

If you have questions please contact Polina Drozdova at p.drozdova@spbu.ru.