Question

scATAC-seq median fragments per cell

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Bogdan ▴ 670

@bogdan-2367

Last seen 13 months ago

Palo Alto, CA, USA

Dear all,

I am using currently a set of BioC/R packages for scATAC-seq analysis, such as Signac, ArchR, SnapATAC, AMULET etc.

As I have just started to use these packages, in order to do the proper filtering, I was wondering :

for a successful scATAC-seq experiment, would you please let me know :

<> what is the standard number of cells,

<> standard value of ATAC-seq median fragments per cell,

I know that it is a question that is not related directly to BioC, I was hoping to get some help please.

Thanks,

Bogdan

ps : I have posted the question also on Biostars, although I have not received any answers yet :

https://www.biostars.org/p/9516233/

SnapATAC Signac ArchR scATAC-seq • 962 views

ADD COMMENT • link 2.7 years ago Bogdan ▴ 670

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Entering edit mode

I have found an answer :

> All Multiome ATAC + GEX datasets
>  
>
> Fresh embryonic E18 mouse brain (5k)
>
> Estimated number of cells: 4,878
> ATAC Mean raw read pairs per cell: 39,755
> ATAC Median high-quality fragments per cell: 16,446
> ATAC Number of peaks: 172,193
> GEX Mean raw reads per cell: 97,172
> GEX Median genes per cell: 3,120
> GEX Median UMI counts per cell: 7,984
> Linked genes: 10,481
> Linked peaks: 56,250
>
> Fresh Frozen Lymph Node with B-cell Lymphoma (14k sorted nuclei)
>
> Estimated number of cells: 14,566
> ATAC Mean raw read pairs per cell: 32,248
> ATAC Median high-quality fragments per cell: 8,396
> ATAC Number of peaks: 109,789
> GEX Mean raw reads per cell: 25,917
> GEX Median genes per cell: 1,186
> GEX Median UMI counts per cell: 1,671
> Linked genes: 12,382
> Linked peaks: 58,474
>
> Frozen human healthy brain tissue (3k)
>
> Estimated number of cells: 3,233
> ATAC Mean raw read pairs per cell: 95,897
> ATAC Median high-quality fragments per cell: 22,881
> ATAC Number of peaks: 134,030
> GEX Mean raw reads per cell: 122,335
> GEX Median genes per cell: 2,600
> GEX Median UMI counts per cell: 6,966
> Linked genes: 13,629
> Linked peaks: 88,843
>
> PBMC from a healthy donor - granulocytes removed through cell sorting (3k)
>
> Estimated number of cells: 2,711
> ATAC Mean raw read pairs per cell: 28,482
> ATAC Median high-quality fragments per cell: 14,479
> ATAC Number of peaks: 98,319
> GEX Mean raw reads per cell: 60,701
> GEX Median genes per cell: 1,791
> GEX Median UMI counts per cell: 3,790
> Linked genes: 8,664
> Linked peaks: 53,127
>
> PBMC from a healthy donor - no cell sorting (10k)
>
> Estimated number of cells: 12,012
> ATAC Mean raw read pairs per cell: 38,103
> ATAC Median high-quality fragments per cell: 11,769
> ATAC Number of peaks: 111,857
> GEX Mean raw reads per cell: 69,129
> GEX Median genes per cell: 1,719
> GEX Median UMI counts per cell: 3,300
> Linked genes: 13,958
> Linked peaks: 79,187

ADD REPLY • link 2.7 years ago Bogdan ▴ 670