computeMatrix to visualize DNA methylation levels

[hzauyangxin]

Why is the DNA methylation level in the output DNA methylation plot from computeMatrix so low, even though I converted my bedGraph file to a bigWig file and used this bw file as input for computeMatrix?

TSS_bed="/home/xyang/index/TSS.genebody.bed"
output_dir="/media/disk2/xyang/cool-seq/bam_files/cx"

computeMatrix scale-regions
-R "$TSS_bed"
-S "$output_dir/IVO.GV/IVO.GV.GCH.bw"
-b 2000 -a 2000
--regionBodyLength 10000
-bs 100
--skipZeros
--missingDataAsZero
-o "$output_dir/test.GCH.matrix.gz"
--outFileNameMatrix "$output_dir/test.GCH.tab"
--outFileSortedRegions "$output_dir/test.GCH.bed"

plotProfile -m /media/disk2/xyang/cool-seq/bam_files/cx/test.GCH.matrix.gz
-out /media/disk2/xyang/cool-seq/bam_files/cx/test.icm.GCH.png
--perGroup
--colors "#D92B03"
--plotTitle "IVO.GCH Profile"
--yAxisLabel "DNA methylation level"
--refPointLabel "TSS"
--samplesLabel "IVO.GV"