AlexsLemonade · jaclyn-taroni · Jul 22, 2021 · Jul 19, 2021 · Jul 19, 2021 · Jul 19, 2021
diff --git a/analyses/focal-cn-file-preparation/02-add-ploidy-consensus.nb.html b/analyses/focal-cn-file-preparation/02-add-ploidy-consensus.nb.html
diff --git a/analyses/focal-cn-file-preparation/03-add-cytoband-status-consensus.nb.html b/analyses/focal-cn-file-preparation/03-add-cytoband-status-consensus.nb.html
diff --git a/analyses/focal-cn-file-preparation/05-define-most-focal-cn-units.nb.html b/analyses/focal-cn-file-preparation/05-define-most-focal-cn-units.nb.html
diff --git a/analyses/focal-cn-file-preparation/06-find-recurrent-calls.nb.html b/analyses/focal-cn-file-preparation/06-find-recurrent-calls.nb.html
diff --git a/analyses/focal-cn-file-preparation/plots/all_histology_cn_counts.png b/analyses/focal-cn-file-preparation/plots/all_histology_cn_counts.png
diff --git a/...-preparation/plots/consensus_seg_annotated_cn_autosomes_polya_loss_cor_plot.png b/...-preparation/plots/consensus_seg_annotated_cn_autosomes_polya_loss_cor_plot.png
diff --git a/...e-preparation/plots/consensus_seg_annotated_cn_autosomes_polya_stacked_plot.png b/...e-preparation/plots/consensus_seg_annotated_cn_autosomes_polya_stacked_plot.png
diff --git a/...eparation/plots/consensus_seg_annotated_cn_autosomes_stranded_loss_cor_plot.png b/...eparation/plots/consensus_seg_annotated_cn_autosomes_stranded_loss_cor_plot.png
diff --git a/...reparation/plots/consensus_seg_annotated_cn_autosomes_stranded_stacked_plot.png b/...reparation/plots/consensus_seg_annotated_cn_autosomes_stranded_stacked_plot.png
diff --git a/...eparation/plots/consensus_seg_annotated_cn_autosomes_stranded_zero_cor_plot.png b/...eparation/plots/consensus_seg_annotated_cn_autosomes_stranded_zero_cor_plot.png
diff --git a/...preparation/plots/consensus_seg_annotated_cn_x_and_y_stranded_loss_cor_plot.png b/...preparation/plots/consensus_seg_annotated_cn_x_and_y_stranded_loss_cor_plot.png
diff --git a/...-preparation/plots/consensus_seg_annotated_cn_x_and_y_stranded_stacked_plot.png b/...-preparation/plots/consensus_seg_annotated_cn_x_and_y_stranded_stacked_plot.png
diff --git a/...preparation/plots/consensus_seg_annotated_cn_x_and_y_stranded_zero_cor_plot.png b/...preparation/plots/consensus_seg_annotated_cn_x_and_y_stranded_zero_cor_plot.png
diff --git a/analyses/focal-cn-file-preparation/plots/separate_histology_cn_counts.png b/analyses/focal-cn-file-preparation/plots/separate_histology_cn_counts.png
diff --git a/analyses/focal-cn-file-preparation/results/consensus_seg_annotated_cn_autosomes.tsv.gz b/analyses/focal-cn-file-preparation/results/consensus_seg_annotated_cn_autosomes.tsv.gz
diff --git a/analyses/focal-cn-file-preparation/results/consensus_seg_annotated_cn_x_and_y.tsv.gz b/analyses/focal-cn-file-preparation/results/consensus_seg_annotated_cn_x_and_y.tsv.gz
diff --git a/analyses/focal-cn-file-preparation/results/consensus_seg_focal_cn_recurrent_genes.tsv b/analyses/focal-cn-file-preparation/results/consensus_seg_focal_cn_recurrent_genes.tsv
@@ -1,24 +1,39 @@
 gene
+KDM7A
+KDM7A-DT
 PARP12
+SLC37A3
 TBXAS1
 TTC26
 UBN2
 ZC3HAV1
+CLEC2L
+FMC1
+FMC1-LUC7L2
+HIPK2
+KLRG2
+LUC7L2
+MKRN1
+RAB19
+ZC3HAV1L
+DENND2A
+KIAA1549
 ADCK2
 BRAF
 CLEC2L
-DENND2A
 FMC1
 FMC1-LUC7L2
 HIPK2
 KDM7A
 KDM7A-DT
-KIAA1549
 KLRG2
 LUC7L2
-MKRN1
 NDUFB2
 NDUFB2-AS1
-RAB19
+PARP12
 SLC37A3
+TBXAS1
+TTC26
+UBN2
+ZC3HAV1
 ZC3HAV1L
diff --git a/analyses/focal-cn-file-preparation/results/consensus_seg_most_focal_cn_status.tsv.gz b/analyses/focal-cn-file-preparation/results/consensus_seg_most_focal_cn_status.tsv.gz