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Commit ab30322c authored by Venkat Malladi's avatar Venkat Malladi
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Update saved files.

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ChIP-seq.sh
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......@@ -154,8 +154,7 @@ plotHeatmap -m matrix_er-alpha.gz -out pj34_heatmap.png --colorList '#FCFCF
--whatToShow 'heatmap and colorbar' --zMin 0 --zMax 3 --kmeans 3 --samplesLabel V E PJ PJ+E V E PJ PJ+E --sortUsing mean --xAxisLabel "Peak Center (bp)" --startLabel "Center" --outFileSortedRegions er-alpha_cluster_sotred.bed
# Closes E2 peak
# Closest E2 peak
computeMatrix reference-point --referencePoint center -R closest_luc_e2_eralpha_supp.bed -b 2500 -a 2500 -S /Volumes/project/GCRB/Lee_Lab/s163035/MCF7_ES_PJ34_Shrikanth/Veh_E2_ER-alpha/call-peaks-macs2.sh-2.0.0/experiment_pooled.fc_signal.bw \
/Volumes/project/GCRB/Lee_Lab/s163035/MCF7_ES_PJ34_Shrikanth/E2_ER-alpha/call-peaks-macs2.sh-2.0.0/experiment_pooled.fc_signal.bw /Volumes/project/GCRB/Lee_Lab/s163035/MCF7_ES_PJ34_Shrikanth/PJ34_ER-alpha/call-peaks-macs2.sh-2.0.0/experiment_pooled.fc_signal.bw \
/Volumes/project/GCRB/Lee_Lab/s163035/MCF7_ES_PJ34_Shrikanth/PJ34_E2_ER-alpha/call-peaks-macs2.sh-2.0.0/experiment_pooled.fc_signal.bw \
......@@ -166,55 +165,3 @@ computeMatrix reference-point --referencePoint center -R closest_luc_e2_eralpha_
plotHeatmap -m matrix_er-alpha_closeset.gz -out pj34_heatmap_closest_er.png --colorList '#FCFCFC,#0044FE' '#FCFCFC,#0044FE' '#FCFCFC,#0044FE' '#FCFCFC,#0044FE' '#FCFCFC,#FC0D17' '#FCFCFC,#FC0D17' '#FCFCFC,#FC0D17' '#FCFCFC,#FC0D17' \
--whatToShow 'heatmap and colorbar' --zMin 0 --zMax 3 --kmeans 2 --samplesLabel V E PJ PJ+E V E PJ PJ+E --sortUsing mean --xAxisLabel "Peak Center (bp)" --startLabel "Center" --outFileSortedRegions er-alpha_cluster_sotred_closest.bed
# Merge All FOXA1 peaks
bedops --everything veh_foxa1.sorted.narrowPeak e2_foxa1.sorted.narrowPeak pj34_foxa1.sorted.narrowPeak pj34_e2_foxa1.sorted.narrowPeak | bedops -m --range -1 - > universe_foxa1.bed
computeMatrix reference-point --referencePoint center -R universe_foxa1.bed -b 2500 -a 2500 -S /Volumes/project/GCRB/Lee_Lab/s163035/MCF7_ES_PJ34_Shrikanth/Veh_E2_FOXA1/call-peaks-macs2.sh-2.0.0/experiment_pooled.fc_signal.bw \
/Volumes/project/GCRB/Lee_Lab/s163035/MCF7_ES_PJ34_Shrikanth/E2_FOXA1/call-peaks-macs2.sh-2.0.0/experiment_pooled.fc_signal.bw /Volumes/project/GCRB/Lee_Lab/s163035/MCF7_ES_PJ34_Shrikanth/PJ34_FOXA1/call-peaks-macs2.sh-2.0.0/experiment_pooled.fc_signal.bw \
/Volumes/project/GCRB/Lee_Lab/s163035/MCF7_ES_PJ34_Shrikanth/PJ34_E2_FOXA1/call-peaks-macs2.sh-2.0.0/experiment_pooled.fc_signal.bw \
/Volumes/project/GCRB/Lee_Lab/s163035/MCF7_ES_PJ34_Shrikanth/Veh_E2_ER-alpha/call-peaks-macs2.sh-2.0.0/experiment_pooled.fc_signal.bw \
/Volumes/project/GCRB/Lee_Lab/s163035/MCF7_ES_PJ34_Shrikanth/E2_ER-alpha/call-peaks-macs2.sh-2.0.0/experiment_pooled.fc_signal.bw /Volumes/project/GCRB/Lee_Lab/s163035/MCF7_ES_PJ34_Shrikanth/PJ34_ER-alpha/call-peaks-macs2.sh-2.0.0/experiment_pooled.fc_signal.bw \
/Volumes/project/GCRB/Lee_Lab/s163035/MCF7_ES_PJ34_Shrikanth/PJ34_E2_ER-alpha/call-peaks-macs2.sh-2.0.0/experiment_pooled.fc_signal.bw \
--skipZeros -o matrix_foxa1.gz --outFileSortedRegions regions_foxa1.bed --numberOfProcessors max
plotHeatmap -m matrix_foxa1.gz -out pj34_heatmap_foxa1.png --colorList '#FCFCFC,#FC0D17' '#FCFCFC,#FC0D17' '#FCFCFC,#FC0D17' '#FCFCFC,#FC0D17' '#FCFCFC,#0044FE' '#FCFCFC,#0044FE' '#FCFCFC,#0044FE' '#FCFCFC,#0044FE' \
--whatToShow 'heatmap and colorbar' --zMin 0 --zMax 3 --kmeans 7 --samplesLabel V E PJ PJ+E V E PJ PJ+E --sortUsing mean --xAxisLabel "Peak Center (bp)" --startLabel "Center" --outFileSortedRegions foxa1_cluster_sorted.bed
# Merge FOXA1 and ER pekas
bedops --everything veh_foxa1.sorted.narrowPeak e2_foxa1.sorted.narrowPeak pj34_foxa1.sorted.narrowPeak pj34_e2_foxa1.sorted.narrowPeak veh_er-alpha.sorted.narrowPeak e2_er-alpha.sorted.narrowPeak pj34_er-alpha.sorted.narrowPeak pj34_e2_er-alpha.sorted.narrowPeak | bedops -m --range -1 - > univers_er_foxa1.bed
computeMatrix reference-point --referencePoint center -R univers_er_foxa1.bed -b 2500 -a 2500 -S /Volumes/project/GCRB/Lee_Lab/s163035/MCF7_ES_PJ34_Shrikanth/Veh_E2_FOXA1/call-peaks-macs2.sh-2.0.0/experiment_pooled.fc_signal.bw \
/Volumes/project/GCRB/Lee_Lab/s163035/MCF7_ES_PJ34_Shrikanth/E2_FOXA1/call-peaks-macs2.sh-2.0.0/experiment_pooled.fc_signal.bw /Volumes/project/GCRB/Lee_Lab/s163035/MCF7_ES_PJ34_Shrikanth/PJ34_FOXA1/call-peaks-macs2.sh-2.0.0/experiment_pooled.fc_signal.bw \
/Volumes/project/GCRB/Lee_Lab/s163035/MCF7_ES_PJ34_Shrikanth/PJ34_E2_FOXA1/call-peaks-macs2.sh-2.0.0/experiment_pooled.fc_signal.bw \
/Volumes/project/GCRB/Lee_Lab/s163035/MCF7_ES_PJ34_Shrikanth/Veh_E2_ER-alpha/call-peaks-macs2.sh-2.0.0/experiment_pooled.fc_signal.bw \
/Volumes/project/GCRB/Lee_Lab/s163035/MCF7_ES_PJ34_Shrikanth/E2_ER-alpha/call-peaks-macs2.sh-2.0.0/experiment_pooled.fc_signal.bw /Volumes/project/GCRB/Lee_Lab/s163035/MCF7_ES_PJ34_Shrikanth/PJ34_ER-alpha/call-peaks-macs2.sh-2.0.0/experiment_pooled.fc_signal.bw \
/Volumes/project/GCRB/Lee_Lab/s163035/MCF7_ES_PJ34_Shrikanth/PJ34_E2_ER-alpha/call-peaks-macs2.sh-2.0.0/experiment_pooled.fc_signal.bw \
--skipZeros -o matrix_foxa1_er.gz --outFileSortedRegions regions_foxa1_er.bed --numberOfProcessors max
plotHeatmap -m matrix_foxa1_er.gz -out pj34_heatmap_foxa1_er.png --colorList '#FCFCFC,#FC0D17' '#FCFCFC,#FC0D17' '#FCFCFC,#FC0D17' '#FCFCFC,#FC0D17' '#FCFCFC,#0044FE' '#FCFCFC,#0044FE' '#FCFCFC,#0044FE' '#FCFCFC,#0044FE' \
--whatToShow 'heatmap and colorbar' --zMin 0 --zMax 3 --kmeans 3 --samplesLabel V E PJ PJ+E V E PJ PJ+E --sortUsing mean --xAxisLabel "Peak Center (bp)" --startLabel "Center" --outFileSortedRegions foxa1_er_cluster_sorted.bed
# FOXA1 and ER no Pj34
bedops --everything veh_foxa1.sorted.narrowPeak e2_foxa1.sorted.narrowPeak veh_er-alpha.sorted.narrowPeak e2_er-alpha.sorted.narrowPeak | bedops -m --range -1 - > universe_er_foxa1.bed
mergePeaks -d 100 veh_foxa1.sorted.narrowPeak e2_foxa1.sorted.narrowPeak e2_er-alpha.sorted.narrowPeak -prefix test
cut -f2-4 test_e2_foxa1.sorted.narrowPeak | grep -v start > test_e2_foxa1.sorted.bed
cut -f2-4 test_veh_foxa1.sorted.narrowPeak | grep -v start > test_veh_foxa1.sorted.bed
cut -f2-4 test_veh_foxa1.sorted.narrowPeak_e2_foxa1.sorted.narrowPeak | grep -v start > test_veh_foxa1.sorted.narrowPeak_e2_foxa1.sorted.bed
cut -f2-4 test_e2_er-alpha.sorted.narrowPeak | grep -v start > test_e2_er-alpha.sorted.bed
cut -f2-4 test_veh_foxa1.sorted.narrowPeak_e2_foxa1.sorted.narrowPeak_e2_er-alpha.sorted.narrowPeak | grep -v start > test_veh_foxa1.sorted.narrowPeak_e2_foxa1.sorted.narrowPeak_e2_er-alpha.sorted.bed
cut -f2-4 test_e2_foxa1.sorted.narrowPeak_e2_er-alpha.sorted.narrowPeak | grep -v start > test_e2_foxa1.sorted.narrowPeak_e2_er-alpha.sorted.bed
cut -f2-4 test_veh_foxa1.sorted.narrowPeak_e2_er-alpha.sorted.narrowPeak | grep -v start > test_veh_foxa1.sorted.narrowPeak_e2_er-alpha.sorted.bed
computeMatrix reference-point --referencePoint center -R test_e2_foxa1.sorted.bed test_veh_foxa1.sorted.bed test_veh_foxa1.sorted.narrowPeak_e2_foxa1.sorted.bed test_e2_er-alpha.sorted.bed test_veh_foxa1.sorted.narrowPeak_e2_foxa1.sorted.narrowPeak_e2_er-alpha.sorted.bed \
test_e2_foxa1.sorted.narrowPeak_e2_er-alpha.sorted.bed -b 1000 -a 1000 \
-S /Volumes/project/GCRB/Lee_Lab/s163035/MCF7_ES_PJ34_Shrikanth/Veh_E2_FOXA1/call-peaks-macs2.sh-2.0.0/experiment_pooled.fc_signal.bw \
/Volumes/project/GCRB/Lee_Lab/s163035/MCF7_ES_PJ34_Shrikanth/E2_FOXA1/call-peaks-macs2.sh-2.0.0/experiment_pooled.fc_signal.bw \
/Volumes/project/GCRB/Lee_Lab/s163035/MCF7_ES_PJ34_Shrikanth/Veh_E2_ER-alpha/call-peaks-macs2.sh-2.0.0/experiment_pooled.fc_signal.bw \
/Volumes/project/GCRB/Lee_Lab/s163035/MCF7_ES_PJ34_Shrikanth/E2_ER-alpha/call-peaks-macs2.sh-2.0.0/experiment_pooled.fc_signal.bw \
--skipZeros -o matrix_foxa1_er_only.gz --outFileSortedRegions regions_foxa1_er_only.bed --numberOfProcessors max
plotHeatmap -m matrix_foxa1_er_only.gz -out heatmap_foxa1_er-only.png --colorList '#FCFCFC,#FC0D17' '#FCFCFC,#FC0D17' '#FCFCFC,#0044FE' '#FCFCFC,#0044FE' \
--whatToShow 'heatmap and colorbar' --zMin 0 --zMax 3 --samplesLabel V E V E --sortUsing mean --xAxisLabel "Peak Center (bp)" --startLabel "Center" --regionsLabel a b c d e f
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