A Researcher's Guide to Population Genomic Analysis
Preface
About the Author
Motivation
Acknowledgements
Citing this book
Citation
Disclaimer
I Techniques
1
Double digest restriction site associated DNA sequencing (ddRADseq)
1.1
Purpose
1.2
Overview
1.2.1
Extraction
1.2.2
Digestion
1.2.3
Ligation
1.2.4
Size-selection
1.2.5
Polymerase chain reaction (PCR)
1.2.6
Sequence
1.3
References
II Tutorials
2
RNA-seq mapping pipeline
2.1
Purpose
2.2
Files required for this pipeline
2.3
Programs used in this pipeline
2.4
Notes on this pipeline
2.5
Overview
2.6
Quality control with FastQC and Trimmomatic
2.7
Mapping with STAR
2.8
Variant calling
2.8.1
Variant calling steps
2.9
References
3
Introduction to R
3.1
Purpose
3.2
Files required for this pipeline
3.3
Programs used in this pipeline
3.4
Notes on this tutorial
3.5
Overview
3.6
References
4
Data wrangling with R
4.1
Purpose
4.2
Files required for this pipeline
4.3
Programs used in this pipeline
4.4
Notes on this tutorial
4.5
Overview
4.6
References
5
Data analysis and visualization in R
5.1
Purpose
5.2
Files required for this pipeline
5.3
Programs used in this pipeline
5.4
Notes on this tutorial
5.5
Overview
5.6
References
Published with bookdown
The Researcher’s Guide to Population Genomic
4
Data wrangling with R
Written by Keaka Farleigh on August 5th, 2025
Last updated by Keaka Farleigh on August 5th, 2025
4.1
Purpose
4.2
Files required for this pipeline
4.3
Programs used in this pipeline
R
(R core team, 2025)
Rstudio
4.4
Notes on this tutorial
4.5
Overview
4.6
References