Closed denvercal1234GitHub closed 3 months ago
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In the tutorial for RNA velocity analysis (http://htmlpreview.github.io/?https://github.com/satijalab/seurat-wrappers/blob/master/docs/scvelo.html), which was what @mojaveazure in issue #3423 advised to do, it performs clustering on "spliced" counts of the loom objects.
Thus, I tried to subset the same cells and genes from the loom objects matching with the cells and genes from my GEX Seurat object and perform the same clustering workflow. My aim is to have the same clusters by performing clustering workflow on the "spliced" counts from loom objects; however, instead I obtained different clusters compared to those I got from performing the same clustering workflow on GEX "RNA".
QUESTION 1. How should I process loom objects so that we can directly connect the trajectories onto the original clusters of the GEX object?
QUESTION 2. Do we expect the clusters generated by GEX (i.e.,
cellranger count
outputs) and the clusters generated by settingbm[["RNA"]] <- bm[["spliced"]]
(i.e., performing clustering on "spliced" counts) to be the same/similar?Thank you for your help!
Related to #6863, #6869 and #5318