A Minimal Book Example
1
Introduction
1.1
Literature review
1.1.1
Experimental evolution
1.1.2
Guppies as a model of sexual selection
1.1.3
The use of different light environments to simulate environmental changes and as a tool to study sexual selection
1.1.4
The role of genotype on phenotype
1.1.5
The role of epigenotype on phenotype
1.1.6
Methods to perform genomic and methylation profiling
1.2
Aims
1.3
Methods to be used
1.4
Expected results
1.5
Significance of the project
2
Methods
2.1
Experimental System
2.1.1
Animal Collection, Care and Treatment
2.1.2
Ambient Light Treatments
2.2
Sample preparation
2.3
Data Processing (section 2.3)
2.4
Pilot Study/Main QC Charts (section 2.4)
2.4.1
FastQC Charts - Unique, Duplicate, Total Reads, GC Content and Trimmed (section 2.5)
2.4.2
Read Length (section 2.5.1)
2.4.3
Insert Length (section 2.5.2)
2.4.4
Methylation (section 2.5.3)
2.4.5
Wasted Bases (section 2.5.4)
2.4.6
Fold Coverage (section 2.5.5)
2.5
Principal Component Analysis and Correlation Heatmaps (section 2.6)
2.6
Differential Methylation Analysis (section 2.7)
2.6.1
dmrseq (section 2.7.1)
2.6.2
Methylkit (section 2.7.2)
2.7
Differential Methylation Figures (section 2.8)
2.8
Identified Tiles (section 2.9)
2.9
Enrichment Analysis
3
Results
3.1
Pilot study QC
3.1.1
Percentage CpG methylation
3.1.2
Insert length
3.1.3
Read length
3.1.4
CpH methylation
3.1.5
Total/Duplicate reads
3.1.6
Wasted bases analysis
3.2
Main data QC
3.2.1
Percentage CpG methylation
3.2.2
Insert Length
3.2.3
Read Length
3.2.4
Total/Duplicate Reads
3.2.5
Wasted bases analysis
3.2.6
Fold coverage
3.3
Principal component analysis and correlation heatmaps
3.4
Differential Methylation Analysis
3.4.1
dmrseq
3.4.2
methylkit
3.5
Enrichment analysis
3.5.1
mitch
3.5.2
Cluster profiler
3.6
Identified tiles
4
Discussion
4.1
Conclusion
5
Abstract
6
Sharing your book
6.1
Publishing
6.2
404 pages
6.3
Metadata for sharing
References
Published with bookdown
Do Methylation Changes Drive the Adaptation to Altered Light Environment in Guppies?
References