Normalization and Differential peaks (Fig 5A, 5D)

[monnieb92]

Hi,

As I am becoming more familiar with NucleoATAC, I am realizing you do not have a way to set a normalization factor, how would you suggest doing that? I used S2 nuclei in my ATAC-Seq to be able to normalize read counts across samples.

In Figure 5A and Figure 5D within the paper there are differential changes in accessibility that you plot in a line plot and heatmap. Is there an output from NucleoATAC that I can use to make a similar figure? Also is there a way to use a normalization factor?

Thank you, Monica

[AdemS80]

Hello,

I am also a NucleoATAC user. I can only suggest that you subsample your bam files for all your samples, so that the number of reads in the subsamples are equal. This is a way of normalizing.