Question: Seurat nFeature_RNA filter number in human
0
gravatar for yueli7
3 months ago by
yueli7110
China
yueli7110 wrote:

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 • 176 views
ADD COMMENTlink written 3 months ago by yueli7110

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

ADD REPLYlink written 3 months ago by ATpoint29k
1

Hello, ATpoint,

Thank you for your response!

There is no suggestion in the tutorial:

https://satijalab.org/seurat/v3.1/pbmc3k_tutorial.html

best,

Yue

ADD REPLYlink written 3 months ago by yueli7110

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

ADD REPLYlink written 3 months ago by yueli7110
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