<p>Looks like a couple options have become available:</p>
<p><strong>Minnow</strong>: <a href="https://academic.oup.com/bioinformatics/article/35/14/i136/5529127?login=true" rel="nofollow noreferrer">article</a> <a href="https://github.com/COMBINE-lab/minnow" rel="nofollow noreferrer">code</a></p>
<p><strong>scReadSim</strong>: <a href="https://www.biorxiv.org/content/10.1101/2022.05.29.493924v1" rel="nofollow noreferrer">preprint</a> <a href="https://github.com/JSB-UCLA/scReadSim" rel="nofollow noreferrer">code</a></p>

CC BY-SA 4.0
2022-06-17T17:58:28.467Z
2022-06-17T18:04:18.287Z
2022-06-17T18:04:18.287Z
merv
<p>Are there any tools that will simulate 3' end tag-based single-cell RNA-seq reads? For example, <code>Drop-seq</code>, <code>10X Chromium</code>, <code>CEL-seq</code>?</p>
<p>There are tools that simulate scRNA-seq gene count data (e.g. <a href="https://genomebiology.biomedcentral.com/articles/10.1186/s13059-017-1305-0" rel="nofollow noreferrer">Splatter</a>), but I can't find anything that will simulate reads or even counts at the transcript level.</p>

<scrnaseq><transcriptome><simulated-data>
Simulating 3' end tag-based scRNA-seq reads
# Simulating 3' end tag-based scRNA-seq reads

(Asked by: username_0 on 2018-10-26)

Are there any tools that will simulate 3' end tag-based single-cell RNA-seq reads? For example, `Drop-seq`, `10X Chromium`, `CEL-seq`?

There are tools that simulate scRNA-seq gene count data (e.g. [Splatter](https://genomebiology.biomedcentral.com/articles/10.1186/s13059-017-1305-0)), but I can't find anything that will simulate reads or even counts at the transcript level.

**Tags:** scrnaseq, transcriptome, simulated-data

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## 1 answers

### Answer by username_0 on 2022-06-17. Score: 1

Looks like a couple options have become available:

**Minnow**: [article](https://academic.oup.com/bioinformatics/article/35/14/i136/5529127?login=true) [code](https://github.com/COMBINE-lab/minnow)

**scReadSim**: [preprint](https://www.biorxiv.org/content/10.1101/2022.05.29.493924v1) [code](https://github.com/JSB-UCLA/scReadSim)


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