Last updated: 2025-05-29

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Knit directory: locust-comparative-genomics/

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    Modified:   data/DEG_results/Bulk_RNAseq/cancellata/Thorax/DESeq2_sigresults_sva_Thorax_cancellata.csv
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    Modified:   data/DEG_results/Bulk_RNAseq/cancellata/Thorax/MA_plot_DEG_Thorax_igris.png
    Modified:   data/DEG_results/Bulk_RNAseq/cancellata/Thorax/MA_plot_DEG_Thorax_igris_togregaria.png
    Modified:   data/DEG_results/Bulk_RNAseq/cancellata/Thorax/PCA_VST_Thorax.png
    Modified:   data/DEG_results/Bulk_RNAseq/cancellata/Thorax/PCA_VST_Thorax_togregaria.png
    Modified:   data/DEG_results/Bulk_RNAseq/cancellata/Thorax/PCA_labelled_VST_Thorax.png
    Modified:   data/DEG_results/Bulk_RNAseq/cancellata/Thorax/PCA_labelled_VST_Thorax_togregaria.png
    Modified:   data/DEG_results/Bulk_RNAseq/cancellata/Thorax/PCA_labelled_normTransform_Thorax.png
    Modified:   data/DEG_results/Bulk_RNAseq/cancellata/Thorax/PCA_labelled_normTransform_Thorax_togregaria.png
    Modified:   data/DEG_results/Bulk_RNAseq/cancellata/Thorax/PCA_labelled_rlog_Thorax.png
    Modified:   data/DEG_results/Bulk_RNAseq/cancellata/Thorax/PCA_labelled_rlog_Thorax_togregaria.png
    Modified:   data/DEG_results/Bulk_RNAseq/cancellata/Thorax/PCA_normTransform_Thorax.png
    Modified:   data/DEG_results/Bulk_RNAseq/cancellata/Thorax/PCA_normTransform_Thorax_togregaria.png
    Modified:   data/DEG_results/Bulk_RNAseq/cancellata/Thorax/PCA_rlog_Thorax.png
    Modified:   data/DEG_results/Bulk_RNAseq/cancellata/Thorax/PCA_rlog_Thorax_togregaria.png
    Modified:   data/DEG_results/Bulk_RNAseq/cancellata/Thorax/heatmap_VST_Thorax.pdf
    Modified:   data/DEG_results/Bulk_RNAseq/cancellata/Thorax/heatmap_VST_Thorax_togregaria.pdf
    Modified:   data/DEG_results/Bulk_RNAseq/cancellata/Thorax/heatmap_normTransform_Thorax.pdf
    Modified:   data/DEG_results/Bulk_RNAseq/cancellata/Thorax/heatmap_normTransform_Thorax_togregaria.pdf
    Modified:   data/DEG_results/Bulk_RNAseq/cancellata/Thorax/heatmap_rlog_Thorax.pdf
    Modified:   data/DEG_results/Bulk_RNAseq/cancellata/Thorax/heatmap_rlog_Thorax_togregaria.pdf
    Modified:   data/DEG_results/Bulk_RNAseq/cancellata/Thorax/sva_scatter_SV1_SV2_Thorax.png
    Modified:   data/DEG_results/Bulk_RNAseq/cancellata/Thorax/sva_scatter_SV1_SV2_Thorax_togregaria.png
    Modified:   data/DEG_results/Bulk_RNAseq/cancellata/Thorax/sva_scatter_SV1_SV3_Thorax.png
    Modified:   data/DEG_results/Bulk_RNAseq/cancellata/Thorax/sva_scatter_SV1_SV3_Thorax_togregaria.png
    Modified:   data/DEG_results/Bulk_RNAseq/cancellata/Thorax/sva_stripchart_SV1_Thorax.png
    Modified:   data/DEG_results/Bulk_RNAseq/cancellata/Thorax/sva_stripchart_SV1_Thorax_togregaria.png
    Modified:   data/DEG_results/Bulk_RNAseq/cancellata/Thorax/sva_stripchart_SV2_Thorax.png
    Modified:   data/DEG_results/Bulk_RNAseq/cancellata/Thorax/sva_stripchart_SV2_Thorax_togregaria.png
    Modified:   data/DEG_results/Bulk_RNAseq/cancellata/Thorax/sva_stripchart_SV3_Thorax.png
    Modified:   data/DEG_results/Bulk_RNAseq/cancellata/Thorax/sva_stripchart_SV3_Thorax_togregaria.png
    Modified:   data/DEG_results/Bulk_RNAseq/cancellata/Thorax/volcano_DEG_Thorax_igris.png
    Modified:   data/DEG_results/Bulk_RNAseq/cancellata/Thorax/volcano_DEG_Thorax_igris_togregaria.png
    Modified:   data/DEG_results/Bulk_RNAseq/cubense/Head/DESeq2_results_sva_Head_cubense.csv
    Modified:   data/DEG_results/Bulk_RNAseq/cubense/Head/DESeq2_results_sva_Head_cubense_togregaria.csv
    Modified:   data/DEG_results/Bulk_RNAseq/cubense/Head/DESeq2_sigresults_sva_Head_cubense.csv
    Modified:   data/DEG_results/Bulk_RNAseq/cubense/Head/DESeq2_sigresults_sva_Head_cubense_togregaria.csv
    Modified:   data/DEG_results/Bulk_RNAseq/cubense/Head/MA_plot_DEG_Head_igris.png
    Modified:   data/DEG_results/Bulk_RNAseq/cubense/Head/MA_plot_DEG_Head_igris_togregaria.png
    Modified:   data/DEG_results/Bulk_RNAseq/cubense/Head/PCA_VST_Head.png
    Modified:   data/DEG_results/Bulk_RNAseq/cubense/Head/PCA_VST_Head_togregaria.png
    Modified:   data/DEG_results/Bulk_RNAseq/cubense/Head/PCA_labelled_VST_Head.png
    Modified:   data/DEG_results/Bulk_RNAseq/cubense/Head/PCA_labelled_VST_Head_togregaria.png
    Modified:   data/DEG_results/Bulk_RNAseq/cubense/Head/PCA_labelled_normTransform_Head.png
    Modified:   data/DEG_results/Bulk_RNAseq/cubense/Head/PCA_labelled_normTransform_Head_togregaria.png
    Modified:   data/DEG_results/Bulk_RNAseq/cubense/Head/PCA_labelled_rlog_Head.png
    Modified:   data/DEG_results/Bulk_RNAseq/cubense/Head/PCA_labelled_rlog_Head_togregaria.png
    Modified:   data/DEG_results/Bulk_RNAseq/cubense/Head/PCA_normTransform_Head.png
    Modified:   data/DEG_results/Bulk_RNAseq/cubense/Head/PCA_normTransform_Head_togregaria.png
    Modified:   data/DEG_results/Bulk_RNAseq/cubense/Head/PCA_rlog_Head.png
    Modified:   data/DEG_results/Bulk_RNAseq/cubense/Head/PCA_rlog_Head_togregaria.png
    Modified:   data/DEG_results/Bulk_RNAseq/cubense/Head/heatmap_VST_Head.pdf
    Modified:   data/DEG_results/Bulk_RNAseq/cubense/Head/heatmap_VST_Head_togregaria.pdf
    Modified:   data/DEG_results/Bulk_RNAseq/cubense/Head/heatmap_normTransform_Head.pdf
    Modified:   data/DEG_results/Bulk_RNAseq/cubense/Head/heatmap_normTransform_Head_togregaria.pdf
    Modified:   data/DEG_results/Bulk_RNAseq/cubense/Head/heatmap_rlog_Head.pdf
    Modified:   data/DEG_results/Bulk_RNAseq/cubense/Head/heatmap_rlog_Head_togregaria.pdf
    Modified:   data/DEG_results/Bulk_RNAseq/cubense/Head/sva_scatter_SV1_SV2_Head.png
    Modified:   data/DEG_results/Bulk_RNAseq/cubense/Head/sva_scatter_SV1_SV2_Head_togregaria.png
    Modified:   data/DEG_results/Bulk_RNAseq/cubense/Head/sva_scatter_SV1_SV3_Head.png
    Modified:   data/DEG_results/Bulk_RNAseq/cubense/Head/sva_scatter_SV1_SV3_Head_togregaria.png
    Modified:   data/DEG_results/Bulk_RNAseq/cubense/Head/sva_scatter_SV2_SV3_Head.png
    Modified:   data/DEG_results/Bulk_RNAseq/cubense/Head/sva_scatter_SV2_SV3_Head_togregaria.png
    Modified:   data/DEG_results/Bulk_RNAseq/cubense/Head/sva_stripchart_SV1_Head.png
    Modified:   data/DEG_results/Bulk_RNAseq/cubense/Head/sva_stripchart_SV1_Head_togregaria.png
    Modified:   data/DEG_results/Bulk_RNAseq/cubense/Head/sva_stripchart_SV2_Head.png
    Modified:   data/DEG_results/Bulk_RNAseq/cubense/Head/sva_stripchart_SV2_Head_togregaria.png
    Modified:   data/DEG_results/Bulk_RNAseq/cubense/Head/sva_stripchart_SV3_Head.png
    Modified:   data/DEG_results/Bulk_RNAseq/cubense/Head/sva_stripchart_SV3_Head_togregaria.png
    Modified:   data/DEG_results/Bulk_RNAseq/cubense/Head/volcano_DEG_Head_igris.png
    Modified:   data/DEG_results/Bulk_RNAseq/cubense/Head/volcano_DEG_Head_igris_togregaria.png
    Modified:   data/DEG_results/Bulk_RNAseq/cubense/PCA_labelled_VST.png
    Modified:   data/DEG_results/Bulk_RNAseq/cubense/PCA_labelled_VST_togregaria.png
    Modified:   data/DEG_results/Bulk_RNAseq/cubense/Thorax/DESeq2_results_sva_Thorax_cubense.csv
    Modified:   data/DEG_results/Bulk_RNAseq/cubense/Thorax/DESeq2_results_sva_Thorax_cubense_togregaria.csv
    Modified:   data/DEG_results/Bulk_RNAseq/cubense/Thorax/DESeq2_sigresults_sva_Thorax_cubense.csv
    Modified:   data/DEG_results/Bulk_RNAseq/cubense/Thorax/DESeq2_sigresults_sva_Thorax_cubense_togregaria.csv
    Modified:   data/DEG_results/Bulk_RNAseq/cubense/Thorax/MA_plot_DEG_Thorax_igris.png
    Modified:   data/DEG_results/Bulk_RNAseq/cubense/Thorax/MA_plot_DEG_Thorax_igris_togregaria.png
    Modified:   data/DEG_results/Bulk_RNAseq/cubense/Thorax/PCA_VST_Thorax.png
    Modified:   data/DEG_results/Bulk_RNAseq/cubense/Thorax/PCA_VST_Thorax_togregaria.png
    Modified:   data/DEG_results/Bulk_RNAseq/cubense/Thorax/PCA_labelled_VST_Thorax.png
    Modified:   data/DEG_results/Bulk_RNAseq/cubense/Thorax/PCA_labelled_VST_Thorax_togregaria.png
    Modified:   data/DEG_results/Bulk_RNAseq/cubense/Thorax/PCA_labelled_normTransform_Thorax.png
    Modified:   data/DEG_results/Bulk_RNAseq/cubense/Thorax/PCA_labelled_normTransform_Thorax_togregaria.png
    Modified:   data/DEG_results/Bulk_RNAseq/cubense/Thorax/PCA_labelled_rlog_Thorax.png
    Modified:   data/DEG_results/Bulk_RNAseq/cubense/Thorax/PCA_labelled_rlog_Thorax_togregaria.png
    Modified:   data/DEG_results/Bulk_RNAseq/cubense/Thorax/PCA_normTransform_Thorax.png
    Modified:   data/DEG_results/Bulk_RNAseq/cubense/Thorax/PCA_normTransform_Thorax_togregaria.png
    Modified:   data/DEG_results/Bulk_RNAseq/cubense/Thorax/PCA_rlog_Thorax.png
    Modified:   data/DEG_results/Bulk_RNAseq/cubense/Thorax/PCA_rlog_Thorax_togregaria.png
    Modified:   data/DEG_results/Bulk_RNAseq/cubense/Thorax/heatmap_VST_Thorax.pdf
    Modified:   data/DEG_results/Bulk_RNAseq/cubense/Thorax/heatmap_VST_Thorax_togregaria.pdf
    Modified:   data/DEG_results/Bulk_RNAseq/cubense/Thorax/heatmap_normTransform_Thorax.pdf
    Modified:   data/DEG_results/Bulk_RNAseq/cubense/Thorax/heatmap_normTransform_Thorax_togregaria.pdf
    Modified:   data/DEG_results/Bulk_RNAseq/cubense/Thorax/heatmap_rlog_Thorax.pdf
    Modified:   data/DEG_results/Bulk_RNAseq/cubense/Thorax/heatmap_rlog_Thorax_togregaria.pdf
    Modified:   data/DEG_results/Bulk_RNAseq/cubense/Thorax/sva_scatter_SV1_SV2_Thorax.png
    Modified:   data/DEG_results/Bulk_RNAseq/cubense/Thorax/sva_scatter_SV1_SV2_Thorax_togregaria.png
    Modified:   data/DEG_results/Bulk_RNAseq/cubense/Thorax/sva_scatter_SV1_SV3_Thorax.png
    Modified:   data/DEG_results/Bulk_RNAseq/cubense/Thorax/sva_scatter_SV1_SV3_Thorax_togregaria.png
    Modified:   data/DEG_results/Bulk_RNAseq/cubense/Thorax/sva_scatter_SV2_SV3_Thorax_togregaria.png
    Modified:   data/DEG_results/Bulk_RNAseq/cubense/Thorax/sva_stripchart_SV1_Thorax.png
    Modified:   data/DEG_results/Bulk_RNAseq/cubense/Thorax/sva_stripchart_SV1_Thorax_togregaria.png
    Modified:   data/DEG_results/Bulk_RNAseq/cubense/Thorax/sva_stripchart_SV2_Thorax.png
    Modified:   data/DEG_results/Bulk_RNAseq/cubense/Thorax/sva_stripchart_SV2_Thorax_togregaria.png
    Modified:   data/DEG_results/Bulk_RNAseq/cubense/Thorax/sva_stripchart_SV3_Thorax.png
    Modified:   data/DEG_results/Bulk_RNAseq/cubense/Thorax/sva_stripchart_SV3_Thorax_togregaria.png
    Modified:   data/DEG_results/Bulk_RNAseq/cubense/Thorax/volcano_DEG_Thorax_igris.png
    Modified:   data/DEG_results/Bulk_RNAseq/cubense/Thorax/volcano_DEG_Thorax_igris_togregaria.png
    Deleted:    data/DEG_results/Bulk_RNAseq/gregaria/Head/DESeq2_results_Head_gregaria.csv
    Modified:   data/DEG_results/Bulk_RNAseq/gregaria/Head/DESeq2_results_Head_gregaria_togregaria.csv
    Modified:   data/DEG_results/Bulk_RNAseq/gregaria/Head/DESeq2_results_sva_Head_gregaria.csv
    Modified:   data/DEG_results/Bulk_RNAseq/gregaria/Head/DESeq2_results_sva_Head_gregaria_togregaria.csv
    Deleted:    data/DEG_results/Bulk_RNAseq/gregaria/Head/DESeq2_sigresults_Head_gregaria.csv
    Modified:   data/DEG_results/Bulk_RNAseq/gregaria/Head/DESeq2_sigresults_Head_gregaria_togregaria.csv
    Modified:   data/DEG_results/Bulk_RNAseq/gregaria/Head/DESeq2_sigresults_sva_Head_gregaria.csv
    Modified:   data/DEG_results/Bulk_RNAseq/gregaria/Head/DESeq2_sigresults_sva_Head_gregaria_togregaria.csv
    Modified:   data/DEG_results/Bulk_RNAseq/gregaria/Head/MA_plot_DEG_Head_igris.png
    Modified:   data/DEG_results/Bulk_RNAseq/gregaria/Head/MA_plot_DEG_Head_igris_togregaria.png
    Modified:   data/DEG_results/Bulk_RNAseq/gregaria/Head/PCA_VST_Head.png
    Modified:   data/DEG_results/Bulk_RNAseq/gregaria/Head/PCA_VST_Head_togregaria.png
    Modified:   data/DEG_results/Bulk_RNAseq/gregaria/Head/PCA_labelled_VST_Head.png
    Modified:   data/DEG_results/Bulk_RNAseq/gregaria/Head/PCA_labelled_VST_Head_togregaria.png
    Modified:   data/DEG_results/Bulk_RNAseq/gregaria/Head/PCA_labelled_normTransform_Head.png
    Modified:   data/DEG_results/Bulk_RNAseq/gregaria/Head/PCA_labelled_normTransform_Head_togregaria.png
    Modified:   data/DEG_results/Bulk_RNAseq/gregaria/Head/PCA_labelled_rlog_Head.png
    Modified:   data/DEG_results/Bulk_RNAseq/gregaria/Head/PCA_labelled_rlog_Head_togregaria.png
    Modified:   data/DEG_results/Bulk_RNAseq/gregaria/Head/PCA_normTransform_Head.png
    Modified:   data/DEG_results/Bulk_RNAseq/gregaria/Head/PCA_normTransform_Head_togregaria.png
    Modified:   data/DEG_results/Bulk_RNAseq/gregaria/Head/PCA_rlog_Head.png
    Modified:   data/DEG_results/Bulk_RNAseq/gregaria/Head/PCA_rlog_Head_togregaria.png
    Modified:   data/DEG_results/Bulk_RNAseq/gregaria/Head/heatmap_VST_Head.pdf
    Modified:   data/DEG_results/Bulk_RNAseq/gregaria/Head/heatmap_VST_Head_togregaria.pdf
    Modified:   data/DEG_results/Bulk_RNAseq/gregaria/Head/heatmap_normTransform_Head.pdf
    Modified:   data/DEG_results/Bulk_RNAseq/gregaria/Head/heatmap_normTransform_Head_togregaria.pdf
    Modified:   data/DEG_results/Bulk_RNAseq/gregaria/Head/heatmap_rlog_Head.pdf
    Modified:   data/DEG_results/Bulk_RNAseq/gregaria/Head/heatmap_rlog_Head_togregaria.pdf
    Modified:   data/DEG_results/Bulk_RNAseq/gregaria/Head/sva_scatter_SV1_SV2_Head.png
    Modified:   data/DEG_results/Bulk_RNAseq/gregaria/Head/sva_scatter_SV1_SV2_Head_togregaria.png
    Modified:   data/DEG_results/Bulk_RNAseq/gregaria/Head/sva_scatter_SV1_SV3_Head.png
    Modified:   data/DEG_results/Bulk_RNAseq/gregaria/Head/sva_scatter_SV1_SV3_Head_togregaria.png
    Modified:   data/DEG_results/Bulk_RNAseq/gregaria/Head/sva_stripchart_SV1_Head.png
    Modified:   data/DEG_results/Bulk_RNAseq/gregaria/Head/sva_stripchart_SV1_Head_togregaria.png
    Modified:   data/DEG_results/Bulk_RNAseq/gregaria/Head/sva_stripchart_SV2_Head.png
    Modified:   data/DEG_results/Bulk_RNAseq/gregaria/Head/sva_stripchart_SV2_Head_togregaria.png
    Modified:   data/DEG_results/Bulk_RNAseq/gregaria/Head/sva_stripchart_SV3_Head.png
    Modified:   data/DEG_results/Bulk_RNAseq/gregaria/Head/sva_stripchart_SV3_Head_togregaria.png
    Deleted:    data/DEG_results/Bulk_RNAseq/gregaria/Head/sva_stripchart_SV4_Head_togregaria.png
    Modified:   data/DEG_results/Bulk_RNAseq/gregaria/Head/volcano_DEG_Head_igris.png
    Modified:   data/DEG_results/Bulk_RNAseq/gregaria/Head/volcano_DEG_Head_igris_togregaria.png
    Modified:   data/DEG_results/Bulk_RNAseq/gregaria/PCA_labelled_VST.png
    Modified:   data/DEG_results/Bulk_RNAseq/gregaria/PCA_labelled_VST_togregaria.png
    Deleted:    data/DEG_results/Bulk_RNAseq/gregaria/Thorax/DESeq2_results_Thorax_gregaria.csv
    Deleted:    data/DEG_results/Bulk_RNAseq/gregaria/Thorax/DESeq2_results_Thorax_gregaria_togregaria.csv
    Modified:   data/DEG_results/Bulk_RNAseq/gregaria/Thorax/DESeq2_results_sva_Thorax_gregaria.csv
    Modified:   data/DEG_results/Bulk_RNAseq/gregaria/Thorax/DESeq2_results_sva_Thorax_gregaria_togregaria.csv
    Deleted:    data/DEG_results/Bulk_RNAseq/gregaria/Thorax/DESeq2_sigresults_Thorax_gregaria.csv
    Deleted:    data/DEG_results/Bulk_RNAseq/gregaria/Thorax/DESeq2_sigresults_Thorax_gregaria_togregaria.csv
    Modified:   data/DEG_results/Bulk_RNAseq/gregaria/Thorax/DESeq2_sigresults_sva_Thorax_gregaria.csv
    Modified:   data/DEG_results/Bulk_RNAseq/gregaria/Thorax/DESeq2_sigresults_sva_Thorax_gregaria_togregaria.csv
    Modified:   data/DEG_results/Bulk_RNAseq/gregaria/Thorax/MA_plot_DEG_Thorax_igris.png
    Modified:   data/DEG_results/Bulk_RNAseq/gregaria/Thorax/MA_plot_DEG_Thorax_igris_togregaria.png
    Modified:   data/DEG_results/Bulk_RNAseq/gregaria/Thorax/PCA_VST_Thorax.png
    Modified:   data/DEG_results/Bulk_RNAseq/gregaria/Thorax/PCA_VST_Thorax_togregaria.png
    Modified:   data/DEG_results/Bulk_RNAseq/gregaria/Thorax/PCA_labelled_VST_Thorax.png
    Modified:   data/DEG_results/Bulk_RNAseq/gregaria/Thorax/PCA_labelled_VST_Thorax_togregaria.png
    Modified:   data/DEG_results/Bulk_RNAseq/gregaria/Thorax/PCA_labelled_normTransform_Thorax.png
    Modified:   data/DEG_results/Bulk_RNAseq/gregaria/Thorax/PCA_labelled_normTransform_Thorax_togregaria.png
    Modified:   data/DEG_results/Bulk_RNAseq/gregaria/Thorax/PCA_labelled_rlog_Thorax.png
    Modified:   data/DEG_results/Bulk_RNAseq/gregaria/Thorax/PCA_labelled_rlog_Thorax_togregaria.png
    Modified:   data/DEG_results/Bulk_RNAseq/gregaria/Thorax/PCA_normTransform_Thorax.png
    Modified:   data/DEG_results/Bulk_RNAseq/gregaria/Thorax/PCA_normTransform_Thorax_togregaria.png
    Modified:   data/DEG_results/Bulk_RNAseq/gregaria/Thorax/PCA_rlog_Thorax.png
    Modified:   data/DEG_results/Bulk_RNAseq/gregaria/Thorax/PCA_rlog_Thorax_togregaria.png
    Modified:   data/DEG_results/Bulk_RNAseq/gregaria/Thorax/heatmap_VST_Thorax.pdf
    Modified:   data/DEG_results/Bulk_RNAseq/gregaria/Thorax/heatmap_VST_Thorax_togregaria.pdf
    Modified:   data/DEG_results/Bulk_RNAseq/gregaria/Thorax/heatmap_normTransform_Thorax.pdf
    Modified:   data/DEG_results/Bulk_RNAseq/gregaria/Thorax/heatmap_normTransform_Thorax_togregaria.pdf
    Modified:   data/DEG_results/Bulk_RNAseq/gregaria/Thorax/heatmap_rlog_Thorax.pdf
    Modified:   data/DEG_results/Bulk_RNAseq/gregaria/Thorax/heatmap_rlog_Thorax_togregaria.pdf
    Modified:   data/DEG_results/Bulk_RNAseq/gregaria/Thorax/sva_scatter_SV1_SV2_Thorax.png
    Modified:   data/DEG_results/Bulk_RNAseq/gregaria/Thorax/sva_scatter_SV1_SV2_Thorax_togregaria.png
    Modified:   data/DEG_results/Bulk_RNAseq/gregaria/Thorax/sva_scatter_SV1_SV3_Thorax.png
    Modified:   data/DEG_results/Bulk_RNAseq/gregaria/Thorax/sva_scatter_SV1_SV3_Thorax_togregaria.png
    Modified:   data/DEG_results/Bulk_RNAseq/gregaria/Thorax/sva_scatter_SV2_SV3_Thorax.png
    Modified:   data/DEG_results/Bulk_RNAseq/gregaria/Thorax/sva_scatter_SV2_SV3_Thorax_togregaria.png
    Modified:   data/DEG_results/Bulk_RNAseq/gregaria/Thorax/sva_stripchart_SV1_Thorax.png
    Modified:   data/DEG_results/Bulk_RNAseq/gregaria/Thorax/sva_stripchart_SV1_Thorax_togregaria.png
    Modified:   data/DEG_results/Bulk_RNAseq/gregaria/Thorax/sva_stripchart_SV2_Thorax.png
    Modified:   data/DEG_results/Bulk_RNAseq/gregaria/Thorax/sva_stripchart_SV2_Thorax_togregaria.png
    Modified:   data/DEG_results/Bulk_RNAseq/gregaria/Thorax/sva_stripchart_SV3_Thorax.png
    Modified:   data/DEG_results/Bulk_RNAseq/gregaria/Thorax/sva_stripchart_SV3_Thorax_togregaria.png
    Modified:   data/DEG_results/Bulk_RNAseq/gregaria/Thorax/volcano_DEG_Thorax_igris.png
    Modified:   data/DEG_results/Bulk_RNAseq/gregaria/Thorax/volcano_DEG_Thorax_igris_togregaria.png
    Modified:   data/DEG_results/Bulk_RNAseq/nitens/Head/DESeq2_results_sva_Head_nitens.csv
    Modified:   data/DEG_results/Bulk_RNAseq/nitens/Head/DESeq2_results_sva_Head_nitens_togregaria.csv
    Modified:   data/DEG_results/Bulk_RNAseq/nitens/Head/DESeq2_sigresults_sva_Head_nitens.csv
    Modified:   data/DEG_results/Bulk_RNAseq/nitens/Head/DESeq2_sigresults_sva_Head_nitens_togregaria.csv
    Modified:   data/DEG_results/Bulk_RNAseq/nitens/Head/MA_plot_DEG_Head_igris.png
    Modified:   data/DEG_results/Bulk_RNAseq/nitens/Head/MA_plot_DEG_Head_igris_togregaria.png
    Modified:   data/DEG_results/Bulk_RNAseq/nitens/Head/PCA_VST_Head.png
    Modified:   data/DEG_results/Bulk_RNAseq/nitens/Head/PCA_VST_Head_togregaria.png
    Modified:   data/DEG_results/Bulk_RNAseq/nitens/Head/PCA_labelled_VST_Head.png
    Modified:   data/DEG_results/Bulk_RNAseq/nitens/Head/PCA_labelled_VST_Head_togregaria.png
    Modified:   data/DEG_results/Bulk_RNAseq/nitens/Head/PCA_labelled_normTransform_Head.png
    Modified:   data/DEG_results/Bulk_RNAseq/nitens/Head/PCA_labelled_normTransform_Head_togregaria.png
    Modified:   data/DEG_results/Bulk_RNAseq/nitens/Head/PCA_labelled_rlog_Head.png
    Modified:   data/DEG_results/Bulk_RNAseq/nitens/Head/PCA_labelled_rlog_Head_togregaria.png
    Modified:   data/DEG_results/Bulk_RNAseq/nitens/Head/PCA_normTransform_Head.png
    Modified:   data/DEG_results/Bulk_RNAseq/nitens/Head/PCA_normTransform_Head_togregaria.png
    Modified:   data/DEG_results/Bulk_RNAseq/nitens/Head/PCA_rlog_Head.png
    Modified:   data/DEG_results/Bulk_RNAseq/nitens/Head/PCA_rlog_Head_togregaria.png
    Modified:   data/DEG_results/Bulk_RNAseq/nitens/Head/heatmap_VST_Head.pdf
    Modified:   data/DEG_results/Bulk_RNAseq/nitens/Head/heatmap_VST_Head_togregaria.pdf
    Modified:   data/DEG_results/Bulk_RNAseq/nitens/Head/heatmap_normTransform_Head.pdf
    Modified:   data/DEG_results/Bulk_RNAseq/nitens/Head/heatmap_normTransform_Head_togregaria.pdf
    Modified:   data/DEG_results/Bulk_RNAseq/nitens/Head/heatmap_rlog_Head.pdf
    Modified:   data/DEG_results/Bulk_RNAseq/nitens/Head/heatmap_rlog_Head_togregaria.pdf
    Modified:   data/DEG_results/Bulk_RNAseq/nitens/Head/sva_scatter_SV1_SV2_Head.png
    Modified:   data/DEG_results/Bulk_RNAseq/nitens/Head/sva_scatter_SV1_SV2_Head_togregaria.png
    Modified:   data/DEG_results/Bulk_RNAseq/nitens/Head/sva_scatter_SV1_SV3_Head.png
    Modified:   data/DEG_results/Bulk_RNAseq/nitens/Head/sva_scatter_SV1_SV3_Head_togregaria.png
    Modified:   data/DEG_results/Bulk_RNAseq/nitens/Head/sva_scatter_SV2_SV3_Head.png
    Modified:   data/DEG_results/Bulk_RNAseq/nitens/Head/sva_scatter_SV2_SV3_Head_togregaria.png
    Modified:   data/DEG_results/Bulk_RNAseq/nitens/Head/sva_stripchart_SV1_Head.png
    Modified:   data/DEG_results/Bulk_RNAseq/nitens/Head/sva_stripchart_SV1_Head_togregaria.png
    Modified:   data/DEG_results/Bulk_RNAseq/nitens/Head/sva_stripchart_SV2_Head.png
    Modified:   data/DEG_results/Bulk_RNAseq/nitens/Head/sva_stripchart_SV2_Head_togregaria.png
    Modified:   data/DEG_results/Bulk_RNAseq/nitens/Head/sva_stripchart_SV3_Head.png
    Modified:   data/DEG_results/Bulk_RNAseq/nitens/Head/sva_stripchart_SV3_Head_togregaria.png
    Modified:   data/DEG_results/Bulk_RNAseq/nitens/Head/volcano_DEG_Head_igris.png
    Modified:   data/DEG_results/Bulk_RNAseq/nitens/Head/volcano_DEG_Head_igris_togregaria.png
    Modified:   data/DEG_results/Bulk_RNAseq/nitens/PCA_labelled_VST.png
    Modified:   data/DEG_results/Bulk_RNAseq/nitens/PCA_labelled_VST_togregaria.png
    Modified:   data/DEG_results/Bulk_RNAseq/nitens/Thorax/MA_plot_DEG_Thorax_igris.png
    Modified:   data/DEG_results/Bulk_RNAseq/nitens/Thorax/MA_plot_DEG_Thorax_igris_togregaria.png
    Modified:   data/DEG_results/Bulk_RNAseq/nitens/Thorax/PCA_VST_Thorax.png
    Modified:   data/DEG_results/Bulk_RNAseq/nitens/Thorax/PCA_VST_Thorax_togregaria.png
    Modified:   data/DEG_results/Bulk_RNAseq/nitens/Thorax/PCA_labelled_VST_Thorax.png
    Modified:   data/DEG_results/Bulk_RNAseq/nitens/Thorax/PCA_labelled_VST_Thorax_togregaria.png
    Modified:   data/DEG_results/Bulk_RNAseq/nitens/Thorax/PCA_labelled_normTransform_Thorax.png
    Modified:   data/DEG_results/Bulk_RNAseq/nitens/Thorax/PCA_labelled_normTransform_Thorax_togregaria.png
    Modified:   data/DEG_results/Bulk_RNAseq/nitens/Thorax/PCA_labelled_rlog_Thorax.png
    Modified:   data/DEG_results/Bulk_RNAseq/nitens/Thorax/PCA_labelled_rlog_Thorax_togregaria.png
    Modified:   data/DEG_results/Bulk_RNAseq/nitens/Thorax/PCA_normTransform_Thorax.png
    Modified:   data/DEG_results/Bulk_RNAseq/nitens/Thorax/PCA_normTransform_Thorax_togregaria.png
    Modified:   data/DEG_results/Bulk_RNAseq/nitens/Thorax/PCA_rlog_Thorax.png
    Modified:   data/DEG_results/Bulk_RNAseq/nitens/Thorax/PCA_rlog_Thorax_togregaria.png
    Modified:   data/DEG_results/Bulk_RNAseq/nitens/Thorax/heatmap_VST_Thorax.pdf
    Modified:   data/DEG_results/Bulk_RNAseq/nitens/Thorax/heatmap_VST_Thorax_togregaria.pdf
    Modified:   data/DEG_results/Bulk_RNAseq/nitens/Thorax/heatmap_normTransform_Thorax.pdf
    Modified:   data/DEG_results/Bulk_RNAseq/nitens/Thorax/heatmap_normTransform_Thorax_togregaria.pdf
    Modified:   data/DEG_results/Bulk_RNAseq/nitens/Thorax/heatmap_rlog_Thorax.pdf
    Modified:   data/DEG_results/Bulk_RNAseq/nitens/Thorax/heatmap_rlog_Thorax_togregaria.pdf
    Modified:   data/DEG_results/Bulk_RNAseq/nitens/Thorax/sva_scatter_SV1_SV2_Thorax.png
    Modified:   data/DEG_results/Bulk_RNAseq/nitens/Thorax/sva_scatter_SV1_SV2_Thorax_togregaria.png
    Modified:   data/DEG_results/Bulk_RNAseq/nitens/Thorax/sva_scatter_SV1_SV3_Thorax.png
    Modified:   data/DEG_results/Bulk_RNAseq/nitens/Thorax/sva_scatter_SV1_SV3_Thorax_togregaria.png
    Modified:   data/DEG_results/Bulk_RNAseq/nitens/Thorax/sva_scatter_SV2_SV3_Thorax.png
    Modified:   data/DEG_results/Bulk_RNAseq/nitens/Thorax/sva_scatter_SV2_SV3_Thorax_togregaria.png
    Modified:   data/DEG_results/Bulk_RNAseq/nitens/Thorax/sva_stripchart_SV1_Thorax.png
    Modified:   data/DEG_results/Bulk_RNAseq/nitens/Thorax/sva_stripchart_SV1_Thorax_togregaria.png
    Modified:   data/DEG_results/Bulk_RNAseq/nitens/Thorax/sva_stripchart_SV2_Thorax.png
    Modified:   data/DEG_results/Bulk_RNAseq/nitens/Thorax/sva_stripchart_SV2_Thorax_togregaria.png
    Modified:   data/DEG_results/Bulk_RNAseq/nitens/Thorax/sva_stripchart_SV3_Thorax.png
    Modified:   data/DEG_results/Bulk_RNAseq/nitens/Thorax/sva_stripchart_SV3_Thorax_togregaria.png
    Modified:   data/DEG_results/Bulk_RNAseq/nitens/Thorax/volcano_DEG_Thorax_igris.png
    Modified:   data/DEG_results/Bulk_RNAseq/nitens/Thorax/volcano_DEG_Thorax_igris_togregaria.png
    Modified:   data/DEG_results/Bulk_RNAseq/piceifrons/Head/DESeq2_results_sva_Head_piceifrons.csv
    Modified:   data/DEG_results/Bulk_RNAseq/piceifrons/Head/DESeq2_results_sva_Head_piceifrons_togregaria.csv
    Modified:   data/DEG_results/Bulk_RNAseq/piceifrons/Head/DESeq2_sigresults_sva_Head_piceifrons.csv
    Modified:   data/DEG_results/Bulk_RNAseq/piceifrons/Head/DESeq2_sigresults_sva_Head_piceifrons_togregaria.csv
    Modified:   data/DEG_results/Bulk_RNAseq/piceifrons/Head/MA_plot_DEG_Head_igris.png
    Modified:   data/DEG_results/Bulk_RNAseq/piceifrons/Head/MA_plot_DEG_Head_igris_togregaria.png
    Modified:   data/DEG_results/Bulk_RNAseq/piceifrons/Head/PCA_VST_Head.png
    Modified:   data/DEG_results/Bulk_RNAseq/piceifrons/Head/PCA_VST_Head_togregaria.png
    Modified:   data/DEG_results/Bulk_RNAseq/piceifrons/Head/PCA_labelled_VST_Head.png
    Modified:   data/DEG_results/Bulk_RNAseq/piceifrons/Head/PCA_labelled_VST_Head_togregaria.png
    Modified:   data/DEG_results/Bulk_RNAseq/piceifrons/Head/PCA_labelled_normTransform_Head.png
    Modified:   data/DEG_results/Bulk_RNAseq/piceifrons/Head/PCA_labelled_normTransform_Head_togregaria.png
    Modified:   data/DEG_results/Bulk_RNAseq/piceifrons/Head/PCA_labelled_rlog_Head.png
    Modified:   data/DEG_results/Bulk_RNAseq/piceifrons/Head/PCA_labelled_rlog_Head_togregaria.png
    Modified:   data/DEG_results/Bulk_RNAseq/piceifrons/Head/PCA_normTransform_Head.png
    Modified:   data/DEG_results/Bulk_RNAseq/piceifrons/Head/PCA_normTransform_Head_togregaria.png
    Modified:   data/DEG_results/Bulk_RNAseq/piceifrons/Head/PCA_rlog_Head.png
    Modified:   data/DEG_results/Bulk_RNAseq/piceifrons/Head/PCA_rlog_Head_togregaria.png
    Modified:   data/DEG_results/Bulk_RNAseq/piceifrons/Head/heatmap_VST_Head.pdf
    Modified:   data/DEG_results/Bulk_RNAseq/piceifrons/Head/heatmap_VST_Head_togregaria.pdf
    Modified:   data/DEG_results/Bulk_RNAseq/piceifrons/Head/heatmap_normTransform_Head.pdf
    Modified:   data/DEG_results/Bulk_RNAseq/piceifrons/Head/heatmap_normTransform_Head_togregaria.pdf
    Modified:   data/DEG_results/Bulk_RNAseq/piceifrons/Head/heatmap_rlog_Head.pdf
    Modified:   data/DEG_results/Bulk_RNAseq/piceifrons/Head/heatmap_rlog_Head_togregaria.pdf
    Modified:   data/DEG_results/Bulk_RNAseq/piceifrons/Head/sva_scatter_SV1_SV2_Head.png
    Modified:   data/DEG_results/Bulk_RNAseq/piceifrons/Head/sva_scatter_SV1_SV2_Head_togregaria.png
    Modified:   data/DEG_results/Bulk_RNAseq/piceifrons/Head/sva_scatter_SV1_SV3_Head.png
    Modified:   data/DEG_results/Bulk_RNAseq/piceifrons/Head/sva_scatter_SV1_SV3_Head_togregaria.png
    Modified:   data/DEG_results/Bulk_RNAseq/piceifrons/Head/sva_stripchart_SV1_Head.png
    Modified:   data/DEG_results/Bulk_RNAseq/piceifrons/Head/sva_stripchart_SV1_Head_togregaria.png
    Modified:   data/DEG_results/Bulk_RNAseq/piceifrons/Head/sva_stripchart_SV2_Head.png
    Modified:   data/DEG_results/Bulk_RNAseq/piceifrons/Head/sva_stripchart_SV2_Head_togregaria.png
    Modified:   data/DEG_results/Bulk_RNAseq/piceifrons/Head/sva_stripchart_SV3_Head.png
    Modified:   data/DEG_results/Bulk_RNAseq/piceifrons/Head/sva_stripchart_SV3_Head_togregaria.png
    Modified:   data/DEG_results/Bulk_RNAseq/piceifrons/Head/volcano_DEG_Head_igris.png
    Modified:   data/DEG_results/Bulk_RNAseq/piceifrons/Head/volcano_DEG_Head_igris_togregaria.png
    Modified:   data/DEG_results/Bulk_RNAseq/piceifrons/PCA_labelled_VST.png
    Modified:   data/DEG_results/Bulk_RNAseq/piceifrons/PCA_labelled_VST_togregaria.png
    Modified:   data/DEG_results/Bulk_RNAseq/piceifrons/Thorax/DESeq2_results_sva_Thorax_piceifrons.csv
    Modified:   data/DEG_results/Bulk_RNAseq/piceifrons/Thorax/DESeq2_results_sva_Thorax_piceifrons_togregaria.csv
    Modified:   data/DEG_results/Bulk_RNAseq/piceifrons/Thorax/DESeq2_sigresults_sva_Thorax_piceifrons.csv
    Modified:   data/DEG_results/Bulk_RNAseq/piceifrons/Thorax/DESeq2_sigresults_sva_Thorax_piceifrons_togregaria.csv
    Modified:   data/DEG_results/Bulk_RNAseq/piceifrons/Thorax/MA_plot_DEG_Thorax_igris.png
    Modified:   data/DEG_results/Bulk_RNAseq/piceifrons/Thorax/MA_plot_DEG_Thorax_igris_togregaria.png
    Modified:   data/DEG_results/Bulk_RNAseq/piceifrons/Thorax/PCA_VST_Thorax.png
    Modified:   data/DEG_results/Bulk_RNAseq/piceifrons/Thorax/PCA_VST_Thorax_togregaria.png
    Modified:   data/DEG_results/Bulk_RNAseq/piceifrons/Thorax/PCA_labelled_VST_Thorax.png
    Modified:   data/DEG_results/Bulk_RNAseq/piceifrons/Thorax/PCA_labelled_VST_Thorax_togregaria.png
    Modified:   data/DEG_results/Bulk_RNAseq/piceifrons/Thorax/PCA_labelled_normTransform_Thorax.png
    Modified:   data/DEG_results/Bulk_RNAseq/piceifrons/Thorax/PCA_labelled_normTransform_Thorax_togregaria.png
    Modified:   data/DEG_results/Bulk_RNAseq/piceifrons/Thorax/PCA_labelled_rlog_Thorax.png
    Modified:   data/DEG_results/Bulk_RNAseq/piceifrons/Thorax/PCA_labelled_rlog_Thorax_togregaria.png
    Modified:   data/DEG_results/Bulk_RNAseq/piceifrons/Thorax/PCA_normTransform_Thorax.png
    Modified:   data/DEG_results/Bulk_RNAseq/piceifrons/Thorax/PCA_normTransform_Thorax_togregaria.png
    Modified:   data/DEG_results/Bulk_RNAseq/piceifrons/Thorax/PCA_rlog_Thorax.png
    Modified:   data/DEG_results/Bulk_RNAseq/piceifrons/Thorax/PCA_rlog_Thorax_togregaria.png
    Modified:   data/DEG_results/Bulk_RNAseq/piceifrons/Thorax/heatmap_VST_Thorax.pdf
    Modified:   data/DEG_results/Bulk_RNAseq/piceifrons/Thorax/heatmap_VST_Thorax_togregaria.pdf
    Modified:   data/DEG_results/Bulk_RNAseq/piceifrons/Thorax/heatmap_normTransform_Thorax.pdf
    Modified:   data/DEG_results/Bulk_RNAseq/piceifrons/Thorax/heatmap_normTransform_Thorax_togregaria.pdf
    Modified:   data/DEG_results/Bulk_RNAseq/piceifrons/Thorax/heatmap_rlog_Thorax.pdf
    Modified:   data/DEG_results/Bulk_RNAseq/piceifrons/Thorax/heatmap_rlog_Thorax_togregaria.pdf
    Modified:   data/DEG_results/Bulk_RNAseq/piceifrons/Thorax/sva_scatter_SV1_SV2_Thorax.png
    Modified:   data/DEG_results/Bulk_RNAseq/piceifrons/Thorax/sva_scatter_SV1_SV2_Thorax_togregaria.png
    Modified:   data/DEG_results/Bulk_RNAseq/piceifrons/Thorax/sva_scatter_SV1_SV3_Thorax.png
    Modified:   data/DEG_results/Bulk_RNAseq/piceifrons/Thorax/sva_scatter_SV1_SV3_Thorax_togregaria.png
    Modified:   data/DEG_results/Bulk_RNAseq/piceifrons/Thorax/sva_scatter_SV2_SV3_Thorax.png
    Modified:   data/DEG_results/Bulk_RNAseq/piceifrons/Thorax/sva_scatter_SV2_SV3_Thorax_togregaria.png
    Modified:   data/DEG_results/Bulk_RNAseq/piceifrons/Thorax/sva_stripchart_SV1_Thorax.png
    Modified:   data/DEG_results/Bulk_RNAseq/piceifrons/Thorax/sva_stripchart_SV1_Thorax_togregaria.png
    Modified:   data/DEG_results/Bulk_RNAseq/piceifrons/Thorax/sva_stripchart_SV2_Thorax.png
    Modified:   data/DEG_results/Bulk_RNAseq/piceifrons/Thorax/sva_stripchart_SV2_Thorax_togregaria.png
    Modified:   data/DEG_results/Bulk_RNAseq/piceifrons/Thorax/sva_stripchart_SV3_Thorax.png
    Modified:   data/DEG_results/Bulk_RNAseq/piceifrons/Thorax/sva_stripchart_SV3_Thorax_togregaria.png
    Modified:   data/DEG_results/Bulk_RNAseq/piceifrons/Thorax/volcano_DEG_Thorax_igris.png
    Modified:   data/DEG_results/Bulk_RNAseq/piceifrons/Thorax/volcano_DEG_Thorax_igris_togregaria.png
    Modified:   data/WGCNA/input/Bulk_RNAseq/datExpr_Head_americana.csv
    Modified:   data/WGCNA/input/Bulk_RNAseq/datExpr_Head_americana_togregaria.csv
    Modified:   data/WGCNA/input/Bulk_RNAseq/datExpr_Head_cancellata.csv
    Modified:   data/WGCNA/input/Bulk_RNAseq/datExpr_Head_cancellata_togregaria.csv
    Modified:   data/WGCNA/input/Bulk_RNAseq/datExpr_Head_cubense.csv
    Modified:   data/WGCNA/input/Bulk_RNAseq/datExpr_Head_cubense_togregaria.csv
    Modified:   data/WGCNA/input/Bulk_RNAseq/datExpr_Head_gregaria.csv
    Modified:   data/WGCNA/input/Bulk_RNAseq/datExpr_Head_gregaria_togregaria.csv
    Modified:   data/WGCNA/input/Bulk_RNAseq/datExpr_Head_nitens.csv
    Modified:   data/WGCNA/input/Bulk_RNAseq/datExpr_Head_nitens_togregaria.csv
    Modified:   data/WGCNA/input/Bulk_RNAseq/datExpr_Head_piceifrons.csv
    Modified:   data/WGCNA/input/Bulk_RNAseq/datExpr_Head_piceifrons_togregaria.csv
    Modified:   data/WGCNA/input/Bulk_RNAseq/datExpr_Thorax_americana.csv
    Modified:   data/WGCNA/input/Bulk_RNAseq/datExpr_Thorax_americana_togregaria.csv
    Modified:   data/WGCNA/input/Bulk_RNAseq/datExpr_Thorax_cancellata.csv
    Modified:   data/WGCNA/input/Bulk_RNAseq/datExpr_Thorax_cancellata_togregaria.csv
    Modified:   data/WGCNA/input/Bulk_RNAseq/datExpr_Thorax_cubense.csv
    Modified:   data/WGCNA/input/Bulk_RNAseq/datExpr_Thorax_cubense_togregaria.csv
    Modified:   data/WGCNA/input/Bulk_RNAseq/datExpr_Thorax_gregaria.csv
    Modified:   data/WGCNA/input/Bulk_RNAseq/datExpr_Thorax_gregaria_togregaria.csv
    Modified:   data/WGCNA/input/Bulk_RNAseq/datExpr_Thorax_nitens.csv
    Modified:   data/WGCNA/input/Bulk_RNAseq/datExpr_Thorax_nitens_togregaria.csv
    Modified:   data/WGCNA/input/Bulk_RNAseq/datExpr_Thorax_piceifrons.csv
    Modified:   data/WGCNA/input/Bulk_RNAseq/datExpr_Thorax_piceifrons_togregaria.csv
    Modified:   data/behavioral_data/50specimens_allspecies.csv
    Modified:   data/list/allspecies_protein2geneid.tsv
    Deleted:    data/orthofinder/Polyneoptera/Results_I2/Comparative_Genomics_Statistics/Duplications_per_Orthogroup.tsv
    Deleted:    data/orthofinder/Polyneoptera/Results_I2/Comparative_Genomics_Statistics/Duplications_per_Species_Tree_Node.tsv
    Deleted:    data/orthofinder/Polyneoptera/Results_I2/Comparative_Genomics_Statistics/Orthogroups_SpeciesOverlaps.tsv
    Deleted:    data/orthofinder/Polyneoptera/Results_I2/Comparative_Genomics_Statistics/OrthologuesStats_Totals.tsv
    Deleted:    data/orthofinder/Polyneoptera/Results_I2/Comparative_Genomics_Statistics/OrthologuesStats_many-to-many.tsv
    Deleted:    data/orthofinder/Polyneoptera/Results_I2/Comparative_Genomics_Statistics/OrthologuesStats_many-to-one.tsv
    Deleted:    data/orthofinder/Polyneoptera/Results_I2/Comparative_Genomics_Statistics/OrthologuesStats_one-to-many.tsv
    Deleted:    data/orthofinder/Polyneoptera/Results_I2/Comparative_Genomics_Statistics/OrthologuesStats_one-to-one.tsv
    Deleted:    data/orthofinder/Polyneoptera/Results_I2/Comparative_Genomics_Statistics/Statistics_Overall.tsv
    Deleted:    data/orthofinder/Polyneoptera/Results_I2/Comparative_Genomics_Statistics/Statistics_PerSpecies.tsv
    Deleted:    data/orthofinder/Polyneoptera/Results_I2/Log.txt
    Deleted:    data/orthofinder/Polyneoptera/Results_I2/Orthogroups/Orthogroups.GeneCount.tsv
    Deleted:    data/orthofinder/Polyneoptera/Results_I2/Orthogroups/Orthogroups.tsv
    Deleted:    data/orthofinder/Polyneoptera/Results_I2/Orthogroups/Orthogroups.txt
    Deleted:    data/orthofinder/Polyneoptera/Results_I2/Orthogroups/Orthogroups_SingleCopyOrthologues.txt
    Deleted:    data/orthofinder/Polyneoptera/Results_I2/Orthogroups/Orthogroups_UnassignedGenes.tsv
    Deleted:    data/orthofinder/Polyneoptera/Results_I2/Orthogroups/Orthogroups_reprocessed.tsv
    Deleted:    data/orthofinder/Polyneoptera/Results_I2/Orthogroups/Orthogroups_reprocessed.txt
    Deleted:    data/orthofinder/Polyneoptera/Results_I2/Orthogroups_13species_Jan2025.txt
    Deleted:    data/orthofinder/Polyneoptera/Results_I2/Orthogroups_genesprotein_Schisto_Jan2025.txt
    Deleted:    data/orthofinder/Polyneoptera/Results_I2/Orthogroups_genesproteinbiotype_13species_Jan2025.csv
    Deleted:    data/orthofinder/Polyneoptera/Results_I2/Plots_Polyneoptera/VerticalStackedBar_A. simplex.pdf
    Deleted:    data/orthofinder/Polyneoptera/Results_I2/Plots_Polyneoptera/VerticalStackedBar_B. rossius.pdf
    Deleted:    data/orthofinder/Polyneoptera/Results_I2/Plots_Polyneoptera/VerticalStackedBar_C. secundus.pdf
    Deleted:    data/orthofinder/Polyneoptera/Results_I2/Plots_Polyneoptera/VerticalStackedBar_D. australis.pdf
    Deleted:    data/orthofinder/Polyneoptera/Results_I2/Plots_Polyneoptera/VerticalStackedBar_G. bimaculatus.pdf
    Deleted:    data/orthofinder/Polyneoptera/Results_I2/Plots_Polyneoptera/VerticalStackedBar_G. longicornis.pdf
    Deleted:    data/orthofinder/Polyneoptera/Results_I2/Plots_Polyneoptera/VerticalStackedBar_P. americana.pdf
    Deleted:    data/orthofinder/Polyneoptera/Results_I2/Plots_Polyneoptera/VerticalStackedBar_americana.pdf
    Deleted:    data/orthofinder/Polyneoptera/Results_I2/Plots_Polyneoptera/VerticalStackedBar_cancellata.pdf
    Deleted:    data/orthofinder/Polyneoptera/Results_I2/Plots_Polyneoptera/VerticalStackedBar_cubense.pdf
    Deleted:    data/orthofinder/Polyneoptera/Results_I2/Plots_Polyneoptera/VerticalStackedBar_gregaria.pdf
    Deleted:    data/orthofinder/Polyneoptera/Results_I2/Plots_Polyneoptera/VerticalStackedBar_nitens.pdf
    Deleted:    data/orthofinder/Polyneoptera/Results_I2/Plots_Polyneoptera/VerticalStackedBar_piceifrons.pdf
    Deleted:    data/orthofinder/Polyneoptera/Results_I2/SingleCopyOrthogroups_genesprotein_13species_Jan2025.txt
    Deleted:    data/orthofinder/Polyneoptera/Results_I2/Species_Tree/Orthogroups_for_concatenated_alignment.txt
    Deleted:    data/orthofinder/Polyneoptera/Results_I2/Species_Tree/Potential_Rooted_Species_Trees/SpeciesTree_rooted_at_outgroup_0.txt
    Deleted:    data/orthofinder/Polyneoptera/Results_I2/Species_Tree/Potential_Rooted_Species_Trees/SpeciesTree_rooted_at_outgroup_1.txt
    Deleted:    data/orthofinder/Polyneoptera/Results_I2/Species_Tree/Potential_Rooted_Species_Trees/SpeciesTree_rooted_at_outgroup_2.txt
    Deleted:    data/orthofinder/Polyneoptera/Results_I2/Species_Tree/Potential_Rooted_Species_Trees/SpeciesTree_rooted_at_outgroup_3.txt
    Deleted:    data/orthofinder/Polyneoptera/Results_I2/Species_Tree/SpeciesTree_rooted.txt
    Deleted:    data/orthofinder/Polyneoptera/Results_I2/Species_Tree/SpeciesTree_rooted_node_labels.txt
    Deleted:    data/orthofinder/Polyneoptera/Results_I5/Comparative_Genomics_Statistics/Duplications_per_Orthogroup.tsv
    Deleted:    data/orthofinder/Polyneoptera/Results_I5/Comparative_Genomics_Statistics/Duplications_per_Species_Tree_Node.tsv
    Deleted:    data/orthofinder/Polyneoptera/Results_I5/Comparative_Genomics_Statistics/Orthogroups_SpeciesOverlaps.tsv
    Deleted:    data/orthofinder/Polyneoptera/Results_I5/Comparative_Genomics_Statistics/OrthologuesStats_Totals.tsv
    Deleted:    data/orthofinder/Polyneoptera/Results_I5/Comparative_Genomics_Statistics/OrthologuesStats_many-to-many.tsv
    Deleted:    data/orthofinder/Polyneoptera/Results_I5/Comparative_Genomics_Statistics/OrthologuesStats_many-to-one.tsv
    Deleted:    data/orthofinder/Polyneoptera/Results_I5/Comparative_Genomics_Statistics/OrthologuesStats_one-to-many.tsv
    Deleted:    data/orthofinder/Polyneoptera/Results_I5/Comparative_Genomics_Statistics/OrthologuesStats_one-to-one.tsv
    Deleted:    data/orthofinder/Polyneoptera/Results_I5/Comparative_Genomics_Statistics/Statistics_Overall.tsv
    Deleted:    data/orthofinder/Polyneoptera/Results_I5/Comparative_Genomics_Statistics/Statistics_PerSpecies.tsv
    Deleted:    data/orthofinder/Polyneoptera/Results_I5/Log.txt
    Deleted:    data/orthofinder/Polyneoptera/Results_I5/Orthogroups/Orthogroups.GeneCount.tsv
    Deleted:    data/orthofinder/Polyneoptera/Results_I5/Orthogroups/Orthogroups.tsv
    Deleted:    data/orthofinder/Polyneoptera/Results_I5/Orthogroups/Orthogroups.txt
    Deleted:    data/orthofinder/Polyneoptera/Results_I5/Orthogroups/Orthogroups_SingleCopyOrthologues.txt
    Deleted:    data/orthofinder/Polyneoptera/Results_I5/Orthogroups/Orthogroups_UnassignedGenes.tsv
    Deleted:    data/orthofinder/Polyneoptera/Results_I5/Orthogroups/Orthogroups_reprocessed.tsv
    Deleted:    data/orthofinder/Polyneoptera/Results_I5/Orthogroups/Orthogroups_reprocessed.txt
    Deleted:    data/orthofinder/Polyneoptera/Results_I5/Species_Tree/Orthogroups_for_concatenated_alignment.txt
    Deleted:    data/orthofinder/Polyneoptera/Results_I5/Species_Tree/Potential_Rooted_Species_Trees/SpeciesTree_rooted_at_outgroup_0.txt
    Deleted:    data/orthofinder/Polyneoptera/Results_I5/Species_Tree/Potential_Rooted_Species_Trees/SpeciesTree_rooted_at_outgroup_1.txt
    Deleted:    data/orthofinder/Polyneoptera/Results_I5/Species_Tree/Potential_Rooted_Species_Trees/SpeciesTree_rooted_at_outgroup_2.txt
    Deleted:    data/orthofinder/Polyneoptera/Results_I5/Species_Tree/Potential_Rooted_Species_Trees/SpeciesTree_rooted_at_outgroup_3.txt
    Deleted:    data/orthofinder/Polyneoptera/Results_I5/Species_Tree/Potential_Rooted_Species_Trees/SpeciesTree_rooted_at_outgroup_4.txt
    Deleted:    data/orthofinder/Polyneoptera/Results_I5/Species_Tree/SpeciesTree_rooted.txt
    Deleted:    data/orthofinder/Polyneoptera/Results_I5/Species_Tree/SpeciesTree_rooted_node_labels.txt
    Deleted:    data/orthofinder/Polyneoptera/inputurls_13polyneoptera_Jan2025.txt
    Modified:   data/orthofinder/Schistocerca/Results_I2/Orthogroups_Schistocerca_Jan2025.txt
    Deleted:    data/orthofinder/Schistocerca/Results_I2/Orthogroups_genesproteinbiotype_Schistocerca_Jan2025.csv
    Modified:   data/orthofinder/Schistocerca/Results_I2/Plots_Schistocerca/VerticalStackedBar_americana.pdf
    Modified:   data/orthofinder/Schistocerca/Results_I2/Plots_Schistocerca/VerticalStackedBar_cancellata.pdf
    Modified:   data/orthofinder/Schistocerca/Results_I2/Plots_Schistocerca/VerticalStackedBar_cubense.pdf
    Modified:   data/orthofinder/Schistocerca/Results_I2/Plots_Schistocerca/VerticalStackedBar_gregaria.pdf
    Modified:   data/orthofinder/Schistocerca/Results_I2/Plots_Schistocerca/VerticalStackedBar_nitens.pdf
    Modified:   data/orthofinder/Schistocerca/Results_I2/Plots_Schistocerca/VerticalStackedBar_piceifrons.pdf
    Deleted:    data/orthofinder/Schistocerca/Results_I2/SingleCopyOrthogroups_genesprotein_6species_Jan2025.txt
    Deleted:    data/orthofinder/Schistocerca/Results_I5/Comparative_Genomics_Statistics/Duplications_per_Orthogroup.tsv
    Deleted:    data/orthofinder/Schistocerca/Results_I5/Comparative_Genomics_Statistics/Duplications_per_Species_Tree_Node.tsv
    Deleted:    data/orthofinder/Schistocerca/Results_I5/Comparative_Genomics_Statistics/Orthogroups_SpeciesOverlaps.tsv
    Deleted:    data/orthofinder/Schistocerca/Results_I5/Comparative_Genomics_Statistics/OrthologuesStats_Totals.tsv
    Deleted:    data/orthofinder/Schistocerca/Results_I5/Comparative_Genomics_Statistics/OrthologuesStats_many-to-many.tsv
    Deleted:    data/orthofinder/Schistocerca/Results_I5/Comparative_Genomics_Statistics/OrthologuesStats_many-to-one.tsv
    Deleted:    data/orthofinder/Schistocerca/Results_I5/Comparative_Genomics_Statistics/OrthologuesStats_one-to-many.tsv
    Deleted:    data/orthofinder/Schistocerca/Results_I5/Comparative_Genomics_Statistics/OrthologuesStats_one-to-one.tsv
    Deleted:    data/orthofinder/Schistocerca/Results_I5/Comparative_Genomics_Statistics/Statistics_Overall.tsv
    Deleted:    data/orthofinder/Schistocerca/Results_I5/Comparative_Genomics_Statistics/Statistics_PerSpecies.tsv
    Deleted:    data/orthofinder/Schistocerca/Results_I5/Log.txt
    Deleted:    data/orthofinder/Schistocerca/Results_I5/Orthogroups/Orthogroups.GeneCount.tsv
    Deleted:    data/orthofinder/Schistocerca/Results_I5/Orthogroups/Orthogroups.tsv
    Deleted:    data/orthofinder/Schistocerca/Results_I5/Orthogroups/Orthogroups.txt
    Deleted:    data/orthofinder/Schistocerca/Results_I5/Orthogroups/Orthogroups_SingleCopyOrthologues.txt
    Deleted:    data/orthofinder/Schistocerca/Results_I5/Orthogroups/Orthogroups_UnassignedGenes.tsv
    Deleted:    data/orthofinder/Schistocerca/Results_I5/Orthogroups/Orthogroups_reprocessed.tsv
    Deleted:    data/orthofinder/Schistocerca/Results_I5/Orthogroups/Orthogroups_reprocessed.txt
    Deleted:    data/orthofinder/Schistocerca/Results_I5/Species_Tree/Orthogroups_for_concatenated_alignment.txt
    Deleted:    data/orthofinder/Schistocerca/Results_I5/Species_Tree/Potential_Rooted_Species_Trees/SpeciesTree_rooted_at_outgroup_0.txt
    Deleted:    data/orthofinder/Schistocerca/Results_I5/Species_Tree/Potential_Rooted_Species_Trees/SpeciesTree_rooted_at_outgroup_1.txt
    Deleted:    data/orthofinder/Schistocerca/Results_I5/Species_Tree/Potential_Rooted_Species_Trees/SpeciesTree_rooted_at_outgroup_2.txt
    Deleted:    data/orthofinder/Schistocerca/Results_I5/Species_Tree/Potential_Rooted_Species_Trees/SpeciesTree_rooted_at_outgroup_3.txt
    Deleted:    data/orthofinder/Schistocerca/Results_I5/Species_Tree/SpeciesTree_rooted.txt
    Deleted:    data/orthofinder/Schistocerca/Results_I5/Species_Tree/SpeciesTree_rooted_node_labels.txt
    Modified:   data/overlap/Bulk_RNAseq/overlapping_genes_head_thorax_americana.csv
    Modified:   data/overlap/Bulk_RNAseq/overlapping_genes_head_thorax_cancellata.csv
    Modified:   data/overlap/Bulk_RNAseq/overlapping_genes_head_thorax_cubense.csv
    Modified:   data/overlap/Bulk_RNAseq/overlapping_genes_head_thorax_gregaria.csv
    Modified:   data/overlap/Bulk_RNAseq/overlapping_genes_head_thorax_piceifrons.csv
    Modified:   data/overlap/Bulk_RNAseq/scatter_plot_overlapping_genes_americana.png
    Modified:   data/overlap/Bulk_RNAseq/scatter_plot_overlapping_genes_cancellata.png
    Modified:   data/overlap/Bulk_RNAseq/scatter_plot_overlapping_genes_cubense.png
    Modified:   data/overlap/Bulk_RNAseq/scatter_plot_overlapping_genes_gregaria.png
    Modified:   data/overlap/Bulk_RNAseq/scatter_plot_overlapping_genes_piceifrons.png
    Deleted:    data/overlap/summaryPolyneoptera_DEGs_Orthogroups_Feb2025.csv
    Deleted:    data/overlap/summaryPolyneoptera_DEGs_Orthogroups_togregaria_Feb2025.csv
    Deleted:    data/overlap/summarySchistocerca_DEGs_Orthogroups_Feb2025.csv
    Deleted:    data/overlap/summarySchistocerca_DEGs_Orthogroups_togregaria_Feb2025.csv

Note that any generated files, e.g. HTML, png, CSS, etc., are not included in this status report because it is ok for generated content to have uncommitted changes.

There are no past versions. Publish this analysis with wflow_publish() to start tracking its development.

1. BUSCO assessment

To test whether core genes found in Insecta are present in the genomes that we will be analyzing, we run BUSCO to assess our Polyneoptera genome quality as recommended.

We ran in protein mode using the protein files XXX_proteins.faa downloaded from NCBI and stored in the folder 1_RawData using the following custom script for GRACE busco_assess.sh:

#!/bin/bash

#SBATCH --job-name=busco_all_proteins
#SBATCH --time=3-00:00:00
#SBATCH --cpus-per-task=48
#SBATCH --mem=250G
#SBATCH --ntasks=1
#SBATCH --output=busco_allproteins.%j.out
#SBATCH --error=busco_allproteins.%j.err

# Load required modules
module purge
ml GCC/12.2.0 OpenMPI/4.1.4 BUSCO/5.7.1 WebProxy

# Set environment variable for NumExpr to avoid "safe limit of 8"
export NUMEXPR_MAX_THREADS=$SLURM_CPUS_PER_TASK

# Set lineage and mode
LINEAGE=insecta_odb10
MODE=protein

# Set directories
INPUT_DIR=$PWD
OUTPUT_DIR=$PWD/busco_results
mkdir -p $OUTPUT_DIR

# Loop through all *_proteins.faa files
for FILE in ${INPUT_DIR}/*_proteins.faa; do
    BASENAME=$(basename "$FILE" _proteins.faa)
    echo "🔎 Starting BUSCO for: $BASENAME"

    busco -i "$FILE" \
          -o "${BASENAME}_busco" \
          -l "$LINEAGE" \
          -m "$MODE" \
          -c $SLURM_CPUS_PER_TASK \
          --out_path "$OUTPUT_DIR" \
          --force

    echo "✅ BUSCO run complete for $FILE"
done

echo "🎉 All BUSCO protein assessments completed!"

Just launch the script with:

#chmod 777 busco_assess.sh
sbatch busco_assess.sh

For 13 genomes, and using 48 CPUs, the run finished in ~5 hours and only used ~9 Gb of memory. We extracted the results from each species folder busco_results/{SPECIES}_busco/short_summary.specific.insecta_odb10.{SPECIES}_busco.txt.


sessionInfo()
R version 4.4.2 (2024-10-31)
Platform: aarch64-apple-darwin20
Running under: macOS Sequoia 15.5

Matrix products: default
BLAS:   /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/lib/libRblas.0.dylib 
LAPACK: /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/lib/libRlapack.dylib;  LAPACK version 3.12.0

locale:
[1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8

time zone: Asia/Tokyo
tzcode source: internal

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base     

loaded via a namespace (and not attached):
 [1] vctrs_0.6.5       cli_3.6.5         knitr_1.49        rlang_1.1.6      
 [5] xfun_0.51         stringi_1.8.4     promises_1.3.2    jsonlite_1.9.1   
 [9] workflowr_1.7.1   glue_1.8.0        rprojroot_2.0.4   git2r_0.35.0     
[13] htmltools_0.5.8.1 httpuv_1.6.15     sass_0.4.9        rmarkdown_2.29   
[17] evaluate_1.0.3    jquerylib_0.1.4   tibble_3.2.1      fastmap_1.2.0    
[21] yaml_2.3.10       lifecycle_1.0.4   stringr_1.5.1     compiler_4.4.2   
[25] fs_1.6.5          Rcpp_1.0.14       pkgconfig_2.0.3   rstudioapi_0.17.1
[29] later_1.4.1       digest_0.6.37     R6_2.6.1          pillar_1.10.2    
[33] magrittr_2.0.3    bslib_0.9.0       tools_4.4.2       cachem_1.1.0