deeptools Compute reference-point and scale-regions

Question

[RD]

Hi All,

In the image provided, I plotted metagene plots for the TSS and TSS-TES regions using the same BED file. While most parameters remained the same, I noticed differences in the y-axis peak values (In A the highest peak values are 0.60 and in B it's close to 0.54) . Can someone explain why this is happening?

Thank you!

Answer 1

[rfran010]

Output your heatmaps and you can have a better idea why the difference.

These are summary plots that report summary statistics, e.g. mean signal of x regions over each 50bp window.

In the left, all TSSs are centered and there is equal genomic distance before and after the TSS, with 5kb to each side.

In the right, you have squished the TSS-TES to be all the same size, where the left is represented by 5kb, but the right squishes signal from 1-100+kb, so you are averaging over vastly different genomic regions.

[RD]

Thank you for the explanation; now it all makes sense.