Seurat: RNA contamination from drop seq single cell rna seq data

[roofya]

I'm wondering if there is a way to remove the effect of rna contamination of some genes? For some genes which is also the markers of one type of cells, is expressed in most of the cells. Thank you so much for your help.

Best

[amisharin]

https://github.com/constantAmateur/SoupX
https://www.biorxiv.org/content/early/2018/04/20/303727

[roofya]

SoupX is a pre-processing method. As such, there are no functions to load Seurat objects as the input.

[mschilli87]

This could change with https://github.com/satijalab/seurat/issues/586 :wink:

[leonfodoulian]

Hi @roofya,

For the moment, you can extract the required data from the corresponding slot from the Seurat object (i.e. [email protected] or object@data, if you need raw or normalised data, respectively), input the data to SoupX, and then replace the data in the Seurat object.

Best,
Leon

[roofya]

@leonfodoulian
What is the function in SoupX should I put [email protected] as input in SoupX? Thank you

[leonfodoulian]

Hi @roofya,

I have never used SoupX, so I don't know what functions should be used. You can refer to the documents and webpages that @amisharin shared with you. You can also refer to their vignette that you can find in their GitHub page. This, nevertheless, goes beyond the scope of the Seurat package.

Best,
Leon