log10(Unique Fragments) vs TSS enrichment score

[LacquerHed]

Wondering how I should further refine this given the two groups in this plot, eliminate the one on the left?

Thanks.

[rcorces]

I dont like providing advice on individual analyses as much of this is based on your own intuition of your own data. Sorry to not be of more help.

[rcorces]

TSS x Frags plots can show a variety of patterns depending on the cell type, nuclei isolation method, etc. As seen in the manual, we exclude "cells" that pass TSS minimum because we dont believe these to truly be cells. But this is based on intuition rather than a heuristic cutoff.

hope that helps

[LacquerHed]

Yes very helpful thank you.

[LacquerHed]

I should have posted this also earlier but I was asking because my genotype breakdown of the nuclear fragments looks like the following, so I should probably not cut those low ones in the WT sample out as they could represent some actual biology. What do you think?

[rcorces]

As before, I dont want to comment on specific analyses. My reply above still stands.

[LacquerHed]

Thanks again for your help!