How to make the profile line of `deepTools::plotHeatmap` more smooth?

Question

[Dan]

Why the profile line has so many wiggles?
How to make the profile line more smooth?
I assume there are some peaks in the .bed file that are highly repeated, how can I delete those peaks?
Thanks a lot

computeMatrix reference-point --referencePoint center -b 1000 -a 1000 \
--missingDataAsZero \
-bl /lila/data/chen/dan/ref/ENCODE_Blacklist/hg19-blacklist.v1_nochr.bed \
-R readcounts/peaks_enhancer/up.bed \
-S bigwigRPGC/*.bw \
-p 12 \
-o plotHeatmap/DMSO.gz \
--outFileNameMatrix plotHeatmap/DMSO.tab


plotHeatmap  -m plotHeatmap/DMSO.gz \
-out plotHeatmap/DMSO.pdf \
--outFileSortedRegions plotHeatmap/DMSO.bed \
--regionsLabel "up" \
--missingDataColor white \
--dpi 300 \
--colorList 'white,magenta' \
--samplesLabel "DMSO1" "DMSO2" \
"100nM-1" "100nM-2" \
"10nM-1" "10nM-2" \
--yMin 0 \
--zMin 0

Answer 1

[Trivas]

Your issue is with your bed file then, not necessarily with deep tools. I'd look into the bedtools suite to see if you can minimize overlap in your features. Maybe use bedtools overlap as a starting point?

[Dan]

Do you mean I should check the intersections between the peaks in the bed file using bedtools intersect (https://bedtools.readthedocs.io/en/latest/content/tools/intersect.html)? And delete the peaks with intersections? Thanks