Is it possible to run SCENIC+ with only scATAC data (without scRNA)?

[Ziyan-Lin]

Hi SCENIC+ team,

Thanks for the amazing tool! I have couple samples only have scATAC-seq data but not scRNA-seq data. I am wondering would it still be possible to run SCENIC+ on those samples? Can I for example use the gene activity matrix from Signac as the gene expression matrix of scRNA side?
I would be really appreciated if anyone have any suggestions!

Many thanks,
Ziyan

[fatcat-del]

I have same problem as you, i don't know if it makes sense, but it's works

[SeppeDeWinter]

Hi @Ziyan-Lin and @fatcat-del

Yes, this becomes a bit more complicated indeed.
If you are able to link the cells for which you only have scATAC-seq to cell types/states in the scRNA-seq you are able to use them.
See this tutorial for example: https://scenicplus.readthedocs.io/en/latest/mix_melanoma_cell_lines.html.

But this is not super trivial.

I hope this helps,

All the best!

Seppe

[AnasAnsari123]

Hi, is this tutorial is still avilable? I am unable to open this tutorial. It would be great if I get the tutorial file, because i am also having the scATAC data.

[fatcat-del]

it‘s not avilable. you can follow tutorial, and scRNA data could be replaced by RNA activity matrix which inferred by scATAC

[SeppeDeWinter]

Hi both,

You can still find the tutorial here: https://github.com/aertslab/scenicplus/blob/old/notebooks/mix_melanoma_cell_lines.ipynb

Best,
Seppe

[Melody-cell]

Hi, @SeppeDeWinter
I carefully read the tutorial, but how can I get the input data?

Many thanks for your consideration!

[SeppeDeWinter]

Hi @Melody-cell

You can find it on GEO: https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE210745

Best,

Seppe

[Melody-cell]

OK, I have found it now, thanks a lot!