Update Fig. 3C.

ChIP-seq.Rmd

@@ -76,6 +76,10 @@ jpeg('venndigram_suppressed_closest_eralpha.jpg')
 draw.pairwise.venn(area1 = 473, area2 = 469, cross.area = 316 ,fill = c("royal blue", "red"))
 dev.off()
 
+jpeg('venndigram_derepressed_closest_foxa1.jpg')
+draw.pairwise.venn(area1 = 313, area2 = 312, cross.area = 170 ,fill = c("royal blue", "red"))
+dev.off()
+
 
 
 # Supp. Figure 3a

ChIP-seq.sh

@@ -45,12 +45,20 @@ cut -f7-10  pc_down_derepressed_parp_e2_foxa1.bed | sort | uniq | awk 'BEGIN{OFS
 ## Find unique non-overlapping peaks and if overlap at least 50% merge
 bedtools intersect -a closest_luc_e2_eralpha_supp.bed -b closest_parp_e2_eralpha_supp.bed -wa -v -f 0.50 -r > unique_luc_e2_eralpha_supp.bed
 bedtools intersect -a closest_parp_e2_eralpha_supp.bed -b closest_luc_e2_eralpha_supp.bed -wa -v -f 0.50 -r > unique_parp_e2_eralpha_supp.bed
-bedtools intersect -a closest_luc_e2_eralpha_supp.bed -b closest_luc_e2_eralpha_supp.bed -wa -f 0.50 -r >> overlap
-bedtools intersect -a closest_luc_e2_eralpha_supp.bed -b closest_luc_e2_eralpha_supp.bed -wb -f 0.50 -r  >> overlap
+bedtools intersect -a closest_luc_e2_eralpha_supp.bed -b closest_parp_e2_eralpha_supp.bed -wa -f 0.50 -r >> overlap
+bedtools intersect -a closest_luc_e2_eralpha_supp.bed -b closest_parp_e2_eralpha_supp.bed -wb -f 0.50 -r  >> overlap
 sort -k1,1 -k2,2n overlap > overlap_sorted
 cut -f1-3 overlap_sorted | bedtools merge -i - | awk 'BEGIN{OFS="\t"}{$4="Merged_Peak_"NR ; print $0}' - > common_eralpha_supp.bed
 rm overlap overlap_sorted
 
+bedtools intersect -a closest_luc_e2_foxa1_derep.bed -b closest_parp_e2_foxa1_derep.bed -wa -v -f 0.50 -r > unique_luc_e2_foxa1_derep.bed
+bedtools intersect -a closest_parp_e2_foxa1_derep.bed -b closest_luc_e2_foxa1_derep.bed -wa -v -f 0.50 -r > unique_parp_e2_foxa1_derep.bed
+bedtools intersect -a closest_luc_e2_foxa1_derep.bed -b closest_parp_e2_foxa1_derep.bed -wa -f 0.50 -r >> overlap
+bedtools intersect -a closest_luc_e2_foxa1_derep.bed -b closest_parp_e2_foxa1_derep.bed -wb -f 0.50 -r  >> overlap
+sort -k1,1 -k2,2n overlap > overlap_sorted
+cut -f1-3 overlap_sorted | bedtools merge -i - | awk 'BEGIN{OFS="\t"}{$4="Merged_Peak_"NR ; print $0}' - > common_foxa1_derep.bed
+rm overlap overlap_sorted
+
 # Combine replicate bams and index
 samtools merge ChIP-seq_Luc_KD_E2_ER-alpha.bam /Volumes/project/GCRB/Lee_Lab/s163035/ChIP-seq/LUC_KD_E2/FOXA1/align-bowtie.sh-1.0.0/ChIP-seq_Luc_KD_E2-1_FOXA1_ATGTCA_L002_R1_001.fastq.gz.sorted.bam /Volumes/project/GCRB/Lee_Lab/s163035/ChIP-seq/LUC_KD_E2/FOXA1/align-bowtie.sh-1.0.0/ChIP-seq_Luc_KD_E2-2_FOXA1_ATGTCA_L003_R1_001.fastq.gz.sorted.bam
 samtools merge ChIP-seq_PARP-1_KD_E2_ER-alpha.bam /project/GCRB/Lee_Lab/s163035/ChIP-seq/PARP-1_KD_E2/FOXA1/align-bowtie.sh-1.0.0/ChIP-seq_PARP-1_KD_E2-1_FOXA1_CGTACG_L002_R1_001.fastq.gz.sorted.bam /project/GCRB/Lee_Lab/s163035/ChIP-seq/PARP-1_KD_E2/FOXA1/align-bowtie.sh-1.0.0/ChIP-seq_PARP-1_KD_E2-2_FOXA1_CGTACG_L003_R1_001.fastq.gz.sorted.bam