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RNA velocity : loom integration for multiple batches #4

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anshu957 opened this issue Aug 30, 2023 · 0 comments
Open

RNA velocity : loom integration for multiple batches #4

anshu957 opened this issue Aug 30, 2023 · 0 comments

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@anshu957
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Thank you for the excellent and very comprehensive tutorial !
I would like to know one specific thing about RNA velocity. In the tutorial, it is mentioned that the second case (of batch corrections) becomes important for RNA velocity analysis and I was wondering if you have any guidance on how to carry out such analysis. For instance, I've sc-RNAseq data coming from multiple batches which is then processed to get a batch-corrected cell state clustering. Now, for the RNa velocity, I've generate 6 loom files (each coming from a different batch) using velocyto package and I combine them together and then finally merge the combined loom file to the processed Andata object. Is this the right approach or do I need to be careful about batch corrections when combining individual loom files ?

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