Data for publication: Unveiling centromeric retrotransposon dynamics through a high quality rye genome assembly

README Overview A structured version of this repository can be found on GitHub: https://github.com/Wicker-Lab/Rye_centromere_analysis The following directory contains data and scripts for figures Fig. 5, S23, S24 (formally S16*), S25 and S28: Fig_5_a-c_Fig_S23_TE_ageXpos_S25_S28 age_distribution_LTR_Abia_H1 age_distribution_LTR_Abigail_H1 age_distribution_LTR_Cereba_H1 age_distribution_LTR_Quinta_H1 age_distribution_RLG_ScerLo7_Abia age_distribution_RLG_ScerLo7_Abigail age_distribution_RLG_ScerLo7_Cereba age_distribution_RLG_ScerLo7_Quinta centromere_positions_Lo7 EDTA_summary_CS-IAAS Figure_5_panels_a_b_c_Figure_S16.R Figure_S23.R Figure_S25.R Figure_S28.R Lo7_rep_input_100kb_mapping_parameters.log2ratio.bedgraph log_chr_comp_Scer_Lo7_V3_chr7R__x__Scer_Weining_v3_H1_chr7R.tab log_chr_comp_Scer_Lo7_V3_chr7R__x__Scer_Weining_v3_H2_chr7R.tab Scer_Lo7_V3_centromere_EDTA_summary_for_R Scer_Lo7_V3_chr1R_gaps Scer_Lo7_V3_chr2R_gaps Scer_Lo7_V3_chr3R_gaps Scer_Lo7_V3_chr4R_gaps Scer_Lo7_V3_chr5R_gaps Scer_Lo7_V3_chr6R_gaps Scer_Lo7_V3_chr7R_gaps Scer_Lo7_V3_genome_size_list Scer_Weining_v3_H1_chr7R_gaps Scer_Weining_v3_H2_chr7R_gaps Tmon_TA299_centromere_EDTA_summary_for_R WeiningV3.H1_log2ratio.bedgraph WeiningV3.H2_log2ratio.bedgraph The following directory contains data and scripts for figure Fig. S30 (formally S20*): Fig_S20_haplotype_and_TE_PAP_dating annotations_chr_segments.tar.gz annotation_TE_PAP_Lo7_x_H2_x_H1 assemble Biomodule.pm blast_compare_chromosome BLOSUM62 chr_comp_date_log_all_orig chr_comp_date_log_all_win400 chr_comp_TE_pos_age_log_all date_from_log_chr_comp Fig_S20_colinearity_species_divergence_TE_PAP.R log_chr_comp_rye_H1_x_H2_Lo7.tar.gz log_chr_comp_rye_Lo7_x_H1_x_H2.tar.gz png_blast_coverage_TE_all positions_colin_segments README_chomosome_colinearity_TE_PAP_analysis.pdf RLG_ScerLo7_Abia_chr7R-438516_TSD TE_PAP_from_log_chr_comp visual_chromosome_compare_dotplot visual_chromosome_compare_segment The following directory contains data and scripts for figure Fig. S31: Fig_S31Scer_TE_expression all_TE_centromere_pos_vs_age_vs_pos feature_counts_compiled_Scer_FR_RLX feature_counts_compiled_Taes_R_RLX Fig_S31Scer_TE_expression.R README_FigS31 * Renumbering occurred during revision process