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txWang / BERMUDA

BERMUDA (Batch Effect ReMoval Using Deep Autoencoders) is a novel transfer-learning-based method for batch correction in scRNA-seq data.
MIT License
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Normalization prior to clustering #2

Closed corticaltone closed 5 years ago

corticaltone commented 5 years ago

Hi Do you normalize the data prior to clustering, or is this done using raw counts?

txWang commented 5 years ago

Hi, We followed the Seurat v2 pipeline to identify cell clusters, which includes normalization before clustering. You could refer to the Seurat toolkit website (https://satijalab.org/seurat/) for more details. Thanks!

corticaltone commented 5 years ago

Thanks!