how to add spliced/unspliced information to my h5ad object

[FADHLyemen]

Hi,
I want to test scvelo but do not have the splice/unsplice in my object in layer, how to add it to my object?

Thank you

[WeilerP]

@FADHLyemen, you can do the following

adata.layers['unspliced'] = unspliced_array
adata.layers['spliced'] = spliced_array

where unspliced_array, spliced_array are numpy.ndarray or sparse matrices.

[FADHLyemen]

Thank you, but how get spliced_array, is it output from cell ranger?

How it look likes? is it a count such X in my h5ad?

Thank you

[WeilerP]

@FADHLyemen you need to run the velocyto pipeline, then read the LOOM file.

In general: Please reply directly to a suggested answer instead of opening a new one which is simply a response to a suggested one.

[FADHLyemen]

@WeilerP
I need to apply scvelo on my data, I have one question on how to get the splice and un-splice information for cells. can I extract it from scRNA-seq or I should have ATAC-seq data to get splice and un-splice to run the velocity program?

[WeilerP]

There is not need for ATAC-seq data. You only need scRNA-seq data.