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I m not sure if I'm going the right way or not but when the gene and region and both upregulated in RNA seq and ATAC seq data I should be seeing a positive correlation but it seems other wise.

Am i doing it in a wrong way or this can occur?

plot

Adding the scatter with points

scatter

Updated Plot

But the issue is with the R^2 value it is very low updated plot

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  • $\begingroup$ this looks like amazing results if true. How many data points do you have? can you add that to the plot or do a heatscatter ? $\endgroup$ – StupidWolf Jan 11 at 1:08
  • $\begingroup$ 1400 UP region and genes ..I okay I will add scatter "this looks like amazing results if true." Im confused.. $\endgroup$ – krushnach Chandra Jan 11 at 5:41
  • $\begingroup$ @StupidWolf updated the plot $\endgroup$ – krushnach Chandra Jan 11 at 5:52
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    $\begingroup$ this looks really weird.. did you flip the direction of the fold change.. and was the data subsetted somehow $\endgroup$ – StupidWolf Jan 11 at 6:18
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    $\begingroup$ the last plot looks about right. most likely you need to subset on genes that are more highly expressed (because the range of the fold change looks crazy), and maybe try promoters for a start $\endgroup$ – StupidWolf Jan 11 at 9:07

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