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