deeptools
Wondering why many sharp peaks created in the deeptools 2.0 heatmap profile
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computeMatrix reference-point
--referencePoint TSS
-b 3000
-a 3000
-R {input.bed}
-S {input.bigwig}
--binSize 50
-o {output}
--outFileSortedRegions {params.dir1} \
plotHeatmap
-m {input}
-out {output}
--interpolationMethod auto
--plotTitle {params}
--colorList 'yellow, red' 'green, blue' \
plotProfile
-m {input}
-out {output}
--plotTitle {params} \
just guessing, but maybe you have regions with extreme outlier bins that drive the average up. try to just plot the top50 regions.
could those be mononucleosomes? there is the one before the TSS and the 3 after that. What kind of data are those?
