<p>Checkout the first <a href="https://satijalab.org/seurat/articles/pbmc3k_tutorial.html" rel="nofollow noreferrer">Seurat tutorial</a>. To filter cells with &gt;20% mitochondrial counts:</p>
<pre><code>obj[[&quot;percent.mito&quot;]] &lt;- PercentageFeatureSet(obj, pattern = &quot;^MT-&quot;)
obj &lt;- subset(obj, subset = percent.mito &lt; 20)
</code></pre>

CC BY-SA 4.0
2021-07-16T16:42:08.270Z
I tried reading the tutorial and things are not really clear there. @Exhausted, when the tutorial says "we filter cells", they mean filtering them out i.e. removing them. So in the `subset` call, one needs to state the criteria that the data needs to pass. It's quite clear that the percent is 1-100, not 0-1 though.
Ram RS
CC BY-SA 4.0
2021-07-15T20:57:29.390Z
2021-07-15T20:57:29.390Z
Chris_Rands
<p>I have extensively read about <code>percent mito</code> in Seurat but I got more and more confused</p>
<p>Let's say we want to keep cells with <code>maximum 20%</code> of their expressed genes are mitochondrial genes, so shall I set <code>percent.mito &lt; 20</code> or <code>percent.mito &lt; 0.2</code> or <code>percent.mito &lt; 80</code> ?</p>

<scrnaseq><seurat><10x-genomics>
What does this Seurat argument mean
# What does this Seurat argument mean

(Asked by: username_0 on 2021-07-15)

I have extensively read about `percent mito` in Seurat but I got more and more confused

Let's say we want to keep cells with `maximum 20%` of their expressed genes are mitochondrial genes, so shall I set `percent.mito < 20` or `percent.mito < 0.2` or `percent.mito < 80` ?

**Tags:** scrnaseq, seurat, 10x-genomics

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## 1 answers

### Answer by username_1 on 2021-07-15. Score: 2 | Accepted answer

Checkout the first Seurat tutorial. To filter cells with >20% mitochondrial counts:
obj[["percent.mito"]] <- PercentageFeatureSet(obj, pattern = "^MT-")
obj <- subset(obj, subset = percent.mito < 20)

> **Comments:**
> **username_2**: I tried reading the tutorial and things are not really clear there. @Exhausted, when the tutorial says "we filter cells", they mean filtering them out i.e. removing them. So in the `subset` call, one needs to state the criteria that the data needs to pass. It's quite clear that the percent is 1-100, not 0-1 though.  

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