Seurat nFeature_RNA filter number in human

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4.5 years ago

yueli7 ▴ 250

Hello, Anyone,

This command in Seurat package means that :

We filter cells that have over 2,500 or less than 200, >5% mitochondrial counts.

If I worked on human, how many unique feature counts we have to filter?

Thanks in advance for great help!

Best,

Yue

pbmc <- subset(pbmc, subset = nFeature_RNA > 200 & nFeature_RNA < 2500 & percent.mt < 5)

RNA-Seq • 2.6k views

ADD COMMENT • link 4.5 years ago by yueli7 ▴ 250

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Why not sticking to what the tutorial suggests if you have no experience?

ADD REPLY • link 4.5 years ago by ATpoint 82k

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Hello, ATpoint,

Thank you for your response！

There is no suggestion in the tutorial:

best,

Yue

ADD REPLY • link 4.5 years ago by yueli7 ▴ 250

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Seurat allows you to easily explore QC metrics and filter cells based on any user-defined criteria.

ADD REPLY • link 4.5 years ago by yueli7 ▴ 250

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