Hello,

I would like to know if the gene order (rows) is maintained along all heatmaps when you perform computeMatrix for several BigWig and BED files followed by plotHeatmap with the --perGroup option. Since I would like to compare the same gene in different samples and regions, I would like to confirm that each row contains information for the same gene.

Here my code:

computeMatrix reference-point -S sample1.bw  sample2.bw  sample3.bw\
                              -R BED_TSS BED_TTS
                              -b 4000 -a 4000 \
                              --missingDataAsZero --maxThreshold 1000 --skipZeros --sortRegions keep 
                               -o output.mat.gz

plotHeatmap -m output.mat.gz --refPointLabel 'TSS TTS' --perGroup --sortUsingSamples 1 2 3 -out output.png

Here the generated heatmaps (left: TSS, right: TTS; up: sample1, mid: sample2, bottom: sample3):

Thank you!