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mbk0asis/deepTools

Last active April 6, 2018 05:24
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deepTools
# Computing matrix
computeMatrix scale-regions -S Muscle.2.bin500.bw Muscle.20.bin500.bw Muscle.28.bin500.bw \
--skipZeros -R mm10/$1.bed -o Muscle.$1.bin500.matrix --outFileNameMatrix Muscle.$1.bin500.matrix.tsv \
-bs 10 -a 5000 -b 5000 --regionBodyLength 10000 \
-–blackListFileName blackList.bed # you may mask specific regions with "black list"
# Plotting heatmap
plotHeatmap -m Muscle.$1.bin500.matrix -out Muscle.$1.bin500.Heatmap.png --colorList 'white,black' # --zMax 10
# Plotting profile
plotProfile -m Muscle.$1.bin500.matrix -out Muscle.$1.bin500.Profile.png --perGroup --averageType mean \
--colors black red blue --plotType se
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