use of Seurat object

[gebdu]

Hi,

can I use Seurat object (with UMAP/clustering already done) just to do the trajectory analysis ?

thanks

[alexQiSong]

Hi,

can I use Seurat object (with UMAP/clustering already done) just to do the trajectory analysis ?

thanks

Hi Gebdu,

Currently loading from Seurat object is not supported yet. But this could be a useful extension. I would consider adding this functionality soon. Thanks for providing the feedback!

Thanks,
Qi

[Dalhte]

Hello there
I extracted the info from my seurat object like this :

write expression counts matrix

library(Matrix)
counts_matrix <- LayerData(object = obj[['RNA']])
writeMM(counts_matrix, file='/counts.mtx')

write gene names

write.table(
data.frame('gene'=rownames(counts_matrix)),file='/gene_names.csv',
quote=F,row.names=F,col.names=F
)

For cell_meta.csv:

I runned velocyto, extracted the anndata obs and variable, and from the obs.csv, keep only the barcodes and the pseudotime index

Cannot say if it is working yet. The files were downloaded successfully, the UMAP reduction is nice, and the inference of trajectory still running (it has been 3 hours now :p)

Best

David

[Dalhte]

Just for you to know that what I proposed above is working in my hands
Best
David