Update Tuesday/Deeptools.md

Tuesday/Deeptools.md

@@ -56,7 +56,21 @@ plotCorrelation \
 # Plot Heatmap
 ## One sample test
 
-From the bw file -> compute matrix prepares an intermediate file that can be used with plot tools  -> plot heatmap
+From the bw file -> compute matrix prepares an intermediate file that can be used with plot functions of deeptools  -> plot heatmap
+compute matrix calculates scores per genome regions, like genes, or user defined regions using one (or more) bed files
+
+computeMatrix scale-regions -S Sample.bw  -R genes.bed --beforeRegionStartLength 3000 --regionBodyLength 5000 --afterRegionStartLength 3000 --skipZeros -o Sample_scale-genes.mat.gz
+
+computeMatrix reference-point -S Sample.bw --referencePoint TSS -R genes.bed --beforeRegionStartLength 3000 --afterRegionStartLength 3000 --skipZeros -o Sample_TSS.mat.gz
+
+
+then plot : 
+
+plotHeatmap -m Sample_scale-genes.mat.gz -out Sample_TSS.pdf
+
+plotProfile -m ample_scale-genes.mat.gz \
+              -out Sample_TSS-ProfileTSS.png \
+              --plotTitle "Test data profile"
 
 
 ## More complex example