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Question about the ambient RNA correction #296

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Chaosli98 opened this issue Aug 22, 2024 · 1 comment
Open

Question about the ambient RNA correction #296

Chaosli98 opened this issue Aug 22, 2024 · 1 comment
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question Further information is requested

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@Chaosli98
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Hi,
First of all, thank you very much for the excellent tutorial. It provides great guidance for professionals in the related field. I have some questions regarding ambient RNA correction:
1.At which point should I perform ambient RNA correction? I noticed that in the current tutorial, low-quality cells and some outliers are removed first before performing ambient RNA correction. Shouldn't ambient RNA correction be done first, followed by cell removal based on pct_counts_mt? Or do you believe the current approach is better?
2.I noticed that ambient RNA correction has not yet been included in the Scanpy tutorial. Is this step essential for droplet-based technologies like 10X?
3.Lastly, I would like to ask about sc.pp.regress_out and sc.pp.scale, which also don't seem to be considered necessary steps in the tutorial. Are these steps recommended? I really look forward to your response, as these questions are crucial for many people who are struggling with different pipelines.

@Chaosli98 Chaosli98 added the question Further information is requested label Aug 22, 2024
@Dexterssssss
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I share the same questions as you and they make me wonder.
I found a youtube video where he reproduces the basic process of scRNA using python and scanpy. I hope this helps: https://www.youtube.com/watch?v=cmOlCTGX4Ik

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