Code and supplementary materials for the manuscript The first high-density linkage map for Australopapuan Treefrogs (Family: Pelodryadidae) reveals the sex determining locus of the Green-eyed Treefrog (Litoria serrata), by Lorenzo V. Bertola, Conrad J. Hoskin, Kyall Zenger, Donald McKnight and Megan Higgie published in Heredity [https://doi.org/10.1038/s41437-023-00642-5].
Structure
In this supplementary material we cover all the code for data processing and analyses. The code is organised in four sections, covering: Data preparation, linkage mapping, summarising linkage maps and identifying sex-linked loci. Follow the links below to see the code for each step.
Data preparation
Linkage mapping with LepMap3
Summarise and display linkage maps
Identify sex-linked loci
Compare linkage map and genome assemblies
R and packages version summary
Thanks for your interest in our paper, whether it comes from a love for frogs or genomics or both!
For further detail on any of the code, please email me!