How to interpret Nucleosome banding pattern in scATAC-Seq?

Question

[patelk26]

Hello,

I am following Signac vignette to perform QC on my single cell ATAC-Seq data. As per my understanding the vignette considers all cells with nucleosome signal > 4 to have a high nucleosomal signal strength and nucleosome signal is calculated by taking a ratio of mononucleosomal to nucleosome-free fragments.

For my data, I see a median nucleosome signal strength for my samples ranging between 0.3 to 0.5. Does that mean my samples have a higher number of nucleosome-free fragments (fragments enriched at TSS) as compared to mononucleosomal region?

I am not sure if I understand how this point towards the quality of the data.

Any help is greatly appreciated!

Khushbu

[Prakki Rama]

Hi @patelk26, could you find an answer to this question?

Answer 1

[Jan]

Hey,

seems like his account is not existing anymore. If anyone else is still interested, I developed a tool evaluating the nucleosomal signal by analysing the strength of the periodical pattern.

Feel free to check it out: Github: https://github.com/loosolab/PEAKQC and Preprint: https://www.biorxiv.org/content/10.1101/2025.02.20.639146v1.full.pdf

Bests, Jan