<jupyter_start><jupyter_text>COMPUTE MATRIX ON MERGED PEAK SET AND PLOT CLUSTERED HEATMAP   H3K4me3<jupyter_code>%%bash

module load deeptools

computeMatrix reference-point -R ../intermediate_files/Merged_Peaks_H3K4me3.bed \
-S ../intermediate_files/Biomek_H3K4me3.filtered.RLEscaled.bw \
../intermediate_files/manual_H3K4me3.filtered.RLEscaled.bw \
--referencePoint center \
--sortRegions keep \
-o ../intermediate_files/H3K4me3_Biomek-Manual_merged.mat.gz \
-b 2000 \
-a 2000 \
--missingDataAsZero \
-p 20 
%%bash

module load deeptools
plotHeatmap -m ../intermediate_files/H3K4me3_Biomek-Manual_merged.mat.gz \
-o ../figures/H3K4me3_Biomek-Manual_merged.pdf --colorList "white,darkred" "white,coral" \
--whatToShow "heatmap and colorbar" \
--kmeans 5<jupyter_output><empty_output><jupyter_text>H3K27ac<jupyter_code>%%bash

module load deeptools

computeMatrix reference-point -R ../intermediate_files/Merged_Peaks_H3K27ac.bed \
-S ../intermediate_files/Biomek_H3K27ac.filtered.RLEscaled.bw \
../intermediate_files/manual_H3K27ac.filtered.RLEscaled.bw \
--referencePoint center \
--sortRegions keep \
-o ../intermediate_files/H3K27ac_Biomek-Manual_merged.mat.gz \
-b 2000 \
-a 2000 \
--missingDataAsZero \
-p 20 
%%bash

module load deeptools
plotHeatmap -m ../intermediate_files/H3K27ac_Biomek-Manual_merged.mat.gz \
-o ../figures/H3K27ac_Biomek-Manual_merged.pdf --colorList "white,darkgreen" "white,limegreen" \
--whatToShow "heatmap and colorbar" \
--kmeans 5<jupyter_output><empty_output><jupyter_text>H3K27me3<jupyter_code>%%bash

module load deeptools

computeMatrix scale-regions -R ../intermediate_files/Merged_Peaks_H3K27me3.bed \
-S ../intermediate_files/Biomek_H3K27me3.filtered.RLEscaled.bw \
../intermediate_files/manual_H3K27me3.filtered.RLEscaled.bw \
--sortRegions keep \
-o ../intermediate_files/H3K27me3_Biomek-Manual_merged.mat.gz \
-b 500 \
-a 500 \
--missingDataAsZero \
-p 20 
%%bash

module load deeptools
plotHeatmap -m ../intermediate_files/H3K27me3_Biomek-Manual_merged.mat.gz \
-o ../figures/H3K27me3_Biomek-Manual_merged.pdf --colorList "white,black" "white,dimgray" \
--whatToShow "heatmap and colorbar" \
--kmeans 5<jupyter_output><empty_output>
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