Multilayered tuning of dosage compensation and Z-chromosome masculinization in the wood white (Leptidea sinapis) butterfly

Pipeline used in:

Lars Höök, Luis Leal, Venkat Talla, Niclas Backström
Genome Biology and Evolution 11(9), 2633–2652 (2019) https://doi.org/10.1093/gbe/evz176

Lars Höök & Luis Leal, Uppsala University, Uppsala, Sweden, 2018-19

Name		Name	Last commit message	Last commit date
Latest commit History 8 Commits
00_Chromosome_mapping_LS2HM		00_Chromosome_mapping_LS2HM
01_Filter_scaffolds		01_Filter_scaffolds
02_Assign_genes_to_chromosome		02_Assign_genes_to_chromosome
03_Normalize_libs		03_Normalize_libs
17_Assign_to_chromosomes_m_vs_f_SBG		17_Assign_to_chromosomes_m_vs_f_SBG
18_Quartile_analysis		18_Quartile_analysis
04_boxplots_a_vs_z.R		04_boxplots_a_vs_z.R
05_dosage_compensation_a_vs_z.R		05_dosage_compensation_a_vs_z.R
06_correlation_and_scatterplot_m_vs_f.R		06_correlation_and_scatterplot_m_vs_f.R
07A_boxplots_individual_chromosomes.R		07A_boxplots_individual_chromosomes.R
07B_dosage_compensation_a_vs_z_indAutosomes.R		07B_dosage_compensation_a_vs_z_indAutosomes.R
08_kruskal-wallis_dunn-test.R		08_kruskal-wallis_dunn-test.R
09_density_plot.R		09_density_plot.R
10_DEseq_analysis_sva.R		10_DEseq_analysis_sva.R
11_volcano_plots.R		11_volcano_plots.R
12_filter_sex_biased_genes.sh		12_filter_sex_biased_genes.sh
13_sex-biased_genes.R		13_sex-biased_genes.R
15_MWU-test_before-vs-after_removing-SBG.R		15_MWU-test_before-vs-after_removing-SBG.R
16A_boxplots_a_vs_z_after_removing_SBG.R		16A_boxplots_a_vs_z_after_removing_SBG.R
16B_boxplots_a_vs_z_SBG.R		16B_boxplots_a_vs_z_SBG.R
19_quartile_analysis_NEW.R		19_quartile_analysis_NEW.R
README.md		README.md
sample_info.txt		sample_info.txt