Chapter 3 | Genetic and methylation variant calling
(2-NILAY john??)
3.1 DMP/DMR Calling in terms of context (CHH, CHG, CG)
3.2 Variant Calling from “Bi-Sulfite Sequencing”
3.3 Different statistical models (HMM,Non Linear / Linear, Bimodal etc.)
Chapter 4 | Transcriptomics
(bumihka??)
4.2 Expression analyses
4.3 Gene Set Enrichment analyses
Chapter 5 | Interpretation
5.1 Graphs
Frontiers
Resources
Chapter 1 | Reference databases
Chapter 2 | Pipelines
Chapter 3 | Scripts
Bibliography
Dowen, R. H., Pelizzola, M., Schmitz, R. J., Lister, R., Dowen, J. M., Nery, J. R., … Ecker, J. R. (2012). Widespread dynamic DNA methylation in response to biotic stress. Proceedings of the National Academy of Sciences of the United States of America, 109(32), E2183–E2191.