reference-point and scale-regions plots vary near the TSS

[Hemantcnaik]

Dear team,

I am using the commands below to generate signal profiles over the TSS region and from TSS to TES. However, I have noticed a difference in the Y-axis values between the TSS and gene body plots. This discrepancy is making it difficult for me to interpret the results.

I also tried using a GTF file, but the outcome remains the same. My BED input file includes strand information, so I’m unsure where the issue might be arising.

I am primarily interested in samples 1 and 2.

Could you please help me understand if there is any mistake in my approach? I would appreciate it if you could review my commands and advise me on how to resolve this issue.

Thank you for your support.

 genebody

   computeMatrix scale-regions -p 10
   -S "Sample1.bw" "Sample2.bw" "Sample3.bw" "Sample4.bw"
   -R genes.bed 
   --regionBodyLength 3000 -b 1500 -a 1500 -bs 100 
   --missingDataAsZero --averageTypeBins mean 
   -o H3K4me1_genebody.gz
   
  TSS
   computeMatrix reference-point -p 10 
   -S  "Sample1.bw" "Sample2.bw" "Sample3.bw" "Sample4.bw"
   -R  genes.bed 
   --referencePoint TSS -b 1500 -a 1500 -bs 100
   --missingDataAsZero --averageTypeBins mean
   -o H3K4me1_TSS.gz

genebody

TSS

with bin size 1 giving me same results. downstream TSS region changing

genebody

TSS