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].

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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

  1. Running stacks
  2. QC Filtering
  3. Segregation distortion
  4. Mendelian filtering
  5. Exporting to LepMap format

Linkage mapping with LepMap3

  1. Separate Chromosomes
  2. Order markers
  3. Check first maps
  4. Polish maps

Summarise and display linkage maps

  1. Summary table S1 - all linkage map markers
  2. Table 1 - linkage map summary
  3. Summary figures

Identify sex-linked loci

  1. Sex-linked loci and producing Fig. 2
  2. Permutation test
  3. GWAS for sex

Compare linkage map and genome assemblies

  1. Linkage map vs assemblies

R and packages version summary

  1. 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!