Commit 10526359 authored by Venkat Malladi's avatar Venkat Malladi
Browse files

Update Fig. 3C.

parent 64eab365
......@@ -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
......
......@@ -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
......
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