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Last update: RNDr. Nataša Šebková, Ph.D. (24.10.2019)
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Last update: RNDr. Nataša Šebková, Ph.D. (24.10.2019)
Cormen, Leiserson, Rivest and Stein. Introduction to Algorithms. 1000 Genomes Project Consortium, A global reference for human genetic variation. Nature. 2015 Oct 1;526(7571):68-74. Rausch et al., Genome sequencing of pediatric medulloblastoma links catastrophic DNA rearrangements with TP53 mutations. Cell. 2012 Jan 20;148(1-2):59-71. Medvedev et al., Computational methods for discovering structural variation with next-generation sequencing. Nat Methods. 2009 Nov;6(11 Suppl):S13-20. Garber M, Grabherr MG, Guttman M, Trapnell C. Computational methods for transcriptome annotation and quantification using RNA-seq. Nat Methods. 2011 Jun;8(6):469-77. doi: 10.1038/nmeth.1613. |
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Last update: RNDr. Nataša Šebková, Ph.D. (24.10.2019)
The exam is a form of home project testing the acquired knowledge and skills after completing the course |
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Last update: RNDr. Nataša Šebková, Ph.D. (25.10.2019)
Areas covered: i) basic alignment, indexing and graph algorithms, data structures ii) tumor genomics - tumor purity, ploidy and heterogeneity (iii) point mutations and 'variant calling' iv) visualization of tumor genomic characteristics (v) approaches to 'comparing' reading to a reference transcriptome or genome vi) approaches to identifying expressed genes and isoforms approaches to estimating isoform frequency and differential expression |
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Last update: RNDr. Nataša Šebková, Ph.D. (24.10.2019)
This course is taught in English. |