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IIRC you expect a lower fraction of mitochondrial genes since you're targeting the nucleus not the whole cell, so adjust QC accordingly. Beyond that, you'll likely see a batch effect if you try to integrate a nuclear and a cellular seq from the same sample. But in terms of analysing the data by Seurat, you shouldn't have any issues as long as you have all the required cellranger outputs. |
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@wudustan ,Hello, sorry to bother you, but I have seen your answer,I don't seem to understand the meaning of this sentence. Do you mean to add the parameter -- included-intron when comparing with the data of scrna-seq? I would appreciate it if you could answer me! |
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Hello all!
As title mentioned, I'm curious about whether snRNA-seq is compatible with scRNA-seq using Seurat.
Sequencing library is 10X chronium, and I used cell ranger.
Are there any tips or cautions for analyzing single nucleus(e.g. dimension reduction)?
I tried to find golden standard, but I could not find good reference.
It is also really helpful if you suggest any good paper :)
Thanks a lot!
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