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.