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scverse / scanpy

Single-cell analysis in Python. Scales to >1M cells.
https://scanpy.readthedocs.io
BSD 3-Clause "New" or "Revised" License
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Integration across SmartSeq2 and 10X Datasets #2662

Closed Teich2233 closed 1 year ago

Teich2233 commented 1 year ago

What kind of feature would you like to request?

Additional function parameters / changed functionality / changed defaults?

Please describe your wishes

Hello,

I am trying to integrate some datasets that were generated with SmartSeq2 and 10X platforms. For the SmartSeq2 datasets, I only got the TPM data, while for the 10x data,I got raw counts matrix. How to merge and integrate SmartSeq2 and 10X Datasets? Can the TPM and raw counts be merged for analysis?

Thank you in advance for your assistance.

Zethson commented 1 year ago

Please ask usage questions here: https://discourse.scverse.org/

You should not integrate normalized and unnormalized counts. Consider getting the raw counts or integrating on the normalized counts

Teich2233 commented 1 year ago

@Zethson Thank you for your help. I know what to do.