How to interpret Nucleosome banding pattern in scATAC-Seq?

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2.5 years ago

patelk26 ▴ 290

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

single-cell scATAC-Seq Signac transcriptomics • 1.2k views

ADD COMMENT • link updated 5 months ago by Prakki Rama ★ 2.7k • written 2.5 years ago by patelk26 ▴ 290