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romanhaa / Cerebro

Visualization of scRNA-seq data.
MIT License
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Input of Monocle trajectory analysis #21

Closed phoebee-h closed 4 years ago

phoebee-h commented 4 years ago

Hi, My name is Phoebe. Thanks for the nice work, with such a clear demonstration! I wonder what's the input in your trajectory step in this README.md? To my knowledge, the "seurat@assays$RNA@data" stores the normalized UMI count matrix, which might not be recommended to import in the Monocle object as I saw here:

image

I supposed "seurat@assays$RNA@counts" would be the suggested one as mentioned above?

Any suggestions would be appreciated. Not sure whether I get it wrong or not. Thank you in advance!

Phoebe

romanhaa commented 4 years ago

Hey Phoebe!

Yes you're right, thank you for pointing that out. I must've missed that and will correct the documentation. Even though it's not really clear to me in which step Monocle performs any normalisation. On the other hand, the Trapnell group advocates using Monocle 3 anyway. I hope I find the time to implement support for results from Monocle 3 at some point.

Best, Roman

phoebee-h commented 4 years ago

Thank you, Roman! :)