Wrong in Deeptools : the enrichment of TSS and TES region are similar when using scale-region
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3 months ago
hao ▴ 10

While using plotProfile to create enrichment for a Pol cut-tag dataset, I got similar enrichment peak around TSS and TES which actully will show higher enrichment in TSS than TES. So could someone help me figure out what wrong in that: enter image description here

And Here is my codes:

computeMatrix scale-regions -p 80 --skipZeros -R xx.bed -S xx.bw -b 2500 -a 2500 --regionBodyLength 2500 -o xx.gz
plotProfile -m xx.gz -out 1xx.pdf --legendLocation upper-right --dpi 750 --perGroup --averageType  mean

Could someone can help fix this? Thank you in advance of the help!

plotprofile computematrix Deeptools scale-region • 420 views
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In the BED file, is there strand information? I should add that if that's not the case then what you're showing is basically what's expected, since there's no way for computeMatrix to know which end of a region is the actual TSS and therefore it has to assume that everything is on the + strand.

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I just saw the news now, and I fixed the problem after adding strand information. And thank you so much!

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