inconsistent peak around TSS between 'reference-point' and 'scale-regions' with plotHeatmap

[ritetsu]

Hello,

While using plotHeatmap to create heatmap for a TF ChIP-seq dataset, I got inconsistent peak around TSS between 'TSS +-3kb region' and 'gene body(TSS-TES) region'.

In figure A, there is a obvious downward trend on the right side of TSS, whereas this phenomenon cannot be observed in figure B. I would like to know if this is it due to the use of reference-point and scale-regions that leads to such discrepancy? Or did I do something wrong?

My deeptools and python version: deeptools 3.5.1 Python 3.6.13 :: Anaconda, Inc.

My codes running deeptools: computeMatrix reference-point -p 8 --referencePoint TSS -b 3000 -a 3000 -R /home/mm10/mm10_GENCODE_vm25.bed --skipZeros -o ./TSS.3kb.gz -S KO.bw WT.bw

computeMatrix scale-regions -p 8 \ -R /home/mm10/mm10_GENCODE_vm25.bed --beforeRegionStartLength 3000 --regionBodyLength 5000 --afterRegionStartLength 3000 --skipZeros -o genebody5kb.gz -S KO.bw WT.bw

plotHeatmap -m ./TSS.3kb.gz -out Heatmap-TSS3kb-y0-25.png --yMin 0 --yMax 10

plotHeatmap -m ./genebody5kb.gz -out Heatmap-TSS-TES-y0-25.png --yMin 0 --yMax 10

Thank you in advance of the help!

[Osynchronika]

Hi, I actually face the same issue, and also with TF ChIP-seq, while histone modifications look alright in both. I am not sure what is happening here... Any help to understand the problem would be great!