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paul_heatmap.bash
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cut -f 1,2,3 /root/ong_dukenus/paul_deseq2/143_over_NT.bed > /root/ong_dukenus/paul_heatmap/143_vs_NT.bed
echo "# 143 specific" >> /root/ong_dukenus/paul_heatmap/143_vs_NT.bed
cut -f 1,2,3 /root/ong_dukenus/paul_deseq2/NT_over_143.bed >> /root/ong_dukenus/paul_heatmap/143_vs_NT.bed
echo "# NT specific" >> /root/ong_dukenus/paul_heatmap/143_vs_NT.bed
computeMatrix reference-point \
-S \
/root/ong_dukenus/paul_bw/1_3502DukeNus_TS543-NT-031117_hg19_i9_rmdup.bw \
/root/ong_dukenus/paul_bw/2_3502DukeNus_TS543-143-031117_hg19_i10_rmdup.bw \
/root/ong_dukenus/paul_bw/3_3502DukeNus_TS543-400-031117_hg19_i11_rmdup.bw \
/root/ong_dukenus/paul_bw/4_3502DukeNus_TS543-NT-241117_hg19_i12_rmdup.bw \
/root/ong_dukenus/paul_bw/5_3502DukeNus_TS543-143-241117_hg19_i13_rmdup.bw \
/root/ong_dukenus/paul_bw/6_3502DukeNus_TS543-400-241117_hg19_i14_rmdup.bw \
-R /root/ong_dukenus/paul_heatmap/143_vs_NT.bed --referencePoint center \
--sortRegions descend -bs 20 -a 1000 -b 1000 -p 40 -out /root/ong_dukenus/paul_heatmap/143_vs_NT.mat
plotHeatmap --xAxisLabel "" --yAxisLabel "" --refPointLabel "ATAC Peak" --colorMap RdBu_r \
-m /root/ong_dukenus/paul_heatmap/143_vs_NT.mat \
--samplesLabel "NT 1" "143 2" "400 3" "NT 4" "143 5" "400 6" \
-out /root/ong_dukenus/paul_heatmap/143_vs_NT_bicolor.pdf
plotHeatmap --xAxisLabel "" --yAxisLabel "" --refPointLabel "ATAC Peak" --colorMap Blues \
-m /root/ong_dukenus/paul_heatmap/143_vs_NT.mat \
--samplesLabel "NT 1" "143 2" "400 3" "NT 4" "143 5" "400 6" \
-out /root/ong_dukenus/paul_heatmap/143_vs_NT_monocolor.pdf
#
cat Up_SH.bed > diff.bed
echo "# SH open" >> diff.bed
cat Down_NT.bed >> diff.bed
echo "# NT Open" >> diff.bed
computeMatrix reference-point \
-S \
/root/ong_dukenus/paul_bw/1_3502DukeNus_TS543-NT-031117_hg19_i9_rmdup.bw \
/root/ong_dukenus/paul_bw/4_3502DukeNus_TS543-NT-241117_hg19_i12_rmdup.bw \
/root/ong_dukenus/paul_bw/2_3502DukeNus_TS543-143-031117_hg19_i10_rmdup.bw \
/root/ong_dukenus/paul_bw/5_3502DukeNus_TS543-143-241117_hg19_i13_rmdup.bw \
/root/ong_dukenus/paul_bw/3_3502DukeNus_TS543-400-031117_hg19_i11_rmdup.bw \
/root/ong_dukenus/paul_bw/6_3502DukeNus_TS543-400-241117_hg19_i14_rmdup.bw \
-R /root/ong_dukenus/paul_diffreps/diff.bed --referencePoint center \
--sortRegions descend -bs 20 -a 1000 -b 1000 -p 40 -out /root/ong_dukenus/paul_heatmap/diffReps.mat
plotHeatmap --xAxisLabel "" --yAxisLabel "" --refPointLabel "ATAC Peak" --colorMap Blues \
-m /root/ong_dukenus/paul_heatmap/diffReps.mat \
--samplesLabel "NT 1" "NT 4" "143 5" "143 2" "400 3" "400 6" \
-out /root/ong_dukenus/paul_heatmap/diffReps.pdf