heatmap看信号分布

scale-regions模式

computeMatrix scale-regions \
-S sample.bw \
-R activate_pro.bed bivalent_pro.bed silenced_pro.bed \
-p 20 \
--skipZeros \
--samplesLabel sample_promoter_binding \
-o sample_scaled.matrix.mat.gz \
--outFileNameMatrix sample_scaled.matrix.tab

plotHeatmap -m sample_scaled.matrix.mat.gz \
--colorMap Blues Oranges Greens Purples \
--plotTitle sample_scaled_binding \
-out sample_scaled_binding.pdf

reference-point模式

computeMatrix reference-point \
-S sample.bw \
-R activate_pro.bed bivalent_pro.bed silenced_pro.bed \
-b 3000 -a 3000 \
--regionBodyLength 5000 \
-p 20 \
--skipZeros \
--samplesLabel sample_promoter_binding \
-o sample_pro_reference.matrix.mat.gz \
--outFileNameMatrix sample_pro_reference.matrix.tab

computeMatrix reference-point \
-S sample.bw \
-R activate_enhancer.bed primed_enhancer.bed poised_enhancer.bed \
-b 3000 -a 3000 \
--regionBodyLength 5000 \
-p 20 \
--skipZeros \
--samplesLabel sample_enhancer_binding \
-o sample_enhancer_reference.matrix.mat.gz \
--outFileNameMatrix  sample_enhancer_reference.matrix.tab

plotHeatmap -m sample_reference.matrix.mat.gz \
--colorMap Greens Oranges Blues Purples \
--plotTitle sample_reference_binding \
-out sample_reference_binding.pdf