Question: Seurat nFeature_RNA filter number in human
0
gravatar for yueli7
23 days ago by
yueli780
China
yueli780 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 • 72 views
ADD COMMENTlink written 23 days ago by yueli780

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

ADD REPLYlink written 23 days ago by ATpoint26k

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 23 days ago by yueli780

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

ADD REPLYlink written 20 days ago by yueli780
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