I have a scRNA data set of we would like to calculate its trajectory.
The data set is splitted into 5 single samples (E.g. c7, g7, h7 etc.). I used cellranger (v. 8.0) to count each of the samples separately. Now I have the *.bc_matrix.h5 files for each of the samples.
I need to run the trajectory analysis on the whole data set, but not sure, how to proceed after the count step.
Should I run velocyto for each of the scRNA-Seq files separately, or it is better to merge them first (and if so, how is it best to do so ,while keeping the original id of each sample)?
I know I can read the files into Seurat using Read10X and CreateSeuratObject, but I'm not sure what to do with the loom files.
Is there somewhere a good tutorial or walk-through for this kind of analysis?
I appreciate any advice.
