smartseq2 RPKM data

[Agnes Forsthuber]

Hi!

I have smartseq2 RPKM data (already analysed with Seurat pipeline) and I want to do trajectory analysis of my cells.

Having RPKM data I wondered whether I can use Monocle 3 or can it just be used with UMI data (10x) ? In Monocle2 it seemed to be possible using relative2abs(), however there are other issues with orderCells():Warning message in if (class(projection) != "matrix") projection <- as.matrix(projection):

“the condition has length > 1 and only the first element will be used”

Since I was not able to overcome this issue - even with changing the source code as described here (https://github.com/cole-trapnell-lab/monocle-release/issues/434) - I wanted to work with monocle3

Is this possible with RPKM data or what is your recommendation to do now?

Thanks Agnes

[Jun-Hoe Lee]

You can try to import the Seurat object into monocle to run pseudotime analysis. 

https://github.com/satijalab/seurat/issues/2833

There's a helpful guide by one of the commenters and tips and tweaks by others.

Good luck!

Kind regards,

Jun-Hoe 

[Agnes Forsthuber]

That worked, thanks! 

However I still wonder whether RMPK data is correct to be used with Monocle3 as I have Smartseq2 data in my SeuratObject and not UMIs as in 10XGenomics. Just to be sure that am using the right format to get correct results. 

Thanks !!! Agnes