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Related to #109, I hope to get some clarification regarding the input data.
I had loom objects for different samples generated by velocyto, and a Seurat object that had been fully analysed (with clustering and UMAP etc).
I was able to concatenate my loom objects into 1 object and converted it to Seurat object, but this object has not been in anyway processed (e.g., normalise etc that are typically done in scVelo pipeline).
Q1. Do I need to process the spliced and unspliced counts somehow before or after adding to my Seurat cluster object?
Q2. How might I add the ambiguous, matrix, spliced, unspliced to my Seurat GEX cluster object? Do I do as below?
Hi @zhanghao-njmu,
Thank you for the package!
Related to #109, I hope to get some clarification regarding the input data.
I had loom objects for different samples generated by
velocyto
, and a Seurat object that had been fully analysed (with clustering and UMAP etc).I was able to concatenate my loom objects into 1 object and converted it to Seurat object, but this object has not been in anyway processed (e.g., normalise etc that are typically done in scVelo pipeline).
Q1. Do I need to process the spliced and unspliced counts somehow before or after adding to my Seurat cluster object?
Q2. How might I add the ambiguous, matrix, spliced, unspliced to my Seurat GEX cluster object? Do I do as below?
Thank you for your help!
My Seurat GEX cluster object:
![Screenshot 2023-05-04 at 18 55 55](https://user-images.githubusercontent.com/62179082/236288722-7b625b17-6ded-4f55-ac0a-ab0b9426197e.png)
My loom-converted Seurat object:
![Screenshot 2023-05-04 at 18 56 04](https://user-images.githubusercontent.com/62179082/236288758-83e34992-9073-4901-8a90-02ba40d6f38b.png)
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