ATAC-seq peaks centered between TSS and TES

Question

[buffealo]

I am analyzing ATAC-seq data and right now trying to confirm my reads enriched around TSS sites however I am obtaining enrichment between TSS and TES for all my samples in two cell lines.

the code I run

computeMatrix reference-point -S m7_rep1.bw -R hg38.TSS.bed --beforeRegionStartLength 1000 --regionBodyLength 2000 --afterRegionStartLength 1000 --binSize 100 -o m7_rep1_matrix.gz; plotHeatmap -m m7_rep1_matrix.gz -out m7_rep1_TSS_enrichment_heatmap.png

I generated the hg38.TSS.bed

awk '$3 == "transcript" {if ($7 == "+") print $1 "\t" $4-1000 "\t" $4+1000; else if ($7 == "-") print $1 "\t" $5-1000 "\t" $5+1000;}' hg38.refGene.gtf > hg38.TSS.bed

I am also not sure about the black genes.

What could be the thing I am doing or is going wrong? I appreciate any help, thank you