<p>As per <a href="https://github.com/broadinstitute/Drop-seq/issues/38#issuecomment-424833407" rel="nofollow noreferrer">this response</a> from Drop-seq_tools team, at the moment intronic regions cannot be annotated and <strong>TagReadWithGeneExon</strong> should be used instead.</p>

<p>However, in the version of the <a href="https://github.com/broadinstitute/Drop-seq" rel="nofollow noreferrer">public repository</a>:</p>

<blockquote>
  <p>TagReadWithGeneExonFunction is the old code, for people who want the more simple tagging methodology and rely on it for 3rd party tools, and TagReadWithGeneFunction, which for your purposes replaces TagReadWithGeneExon. [...]  You’ll see additional options to extract expression for CODING, UTR, INTRONIC reads [...]</p>
</blockquote>

CC BY-SA 4.0
2018-09-27T01:30:12.030Z
2018-09-27T01:30:12.030Z
gc5
<p>I am using <a href="http://mccarrolllab.org/dropseq/" rel="nofollow noreferrer">Drop-seq_tools</a> to analyze scRNA-seq in a similar way of <a href="https://www.ncbi.nlm.nih.gov/pubmed/29227469" rel="nofollow noreferrer">this paper</a>. I am using the <a href="https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE97930" rel="nofollow noreferrer">same data (GSE97930)</a> to get used to Drop-seq_tools.</p>

<p>On the GEO repo the authors provide the relevant code (<a href="https://www.ncbi.nlm.nih.gov/geo/download/?acc=GSE97930&amp;format=file&amp;file=GSE97930%5FREADME%2Etxt" rel="nofollow noreferrer">GSE97930_README.txt</a>). However, one tool used in the script is missing: <strong>TagReadWithGene</strong>.</p>

<p>The latest version of Drop-seq_tools does not have such method (as it should be provided by this library), and there is no version history for the whole package, so I cannot download previous versions.</p>

<p>The best matches for the missing method are <strong>TagReadWithGeneExon</strong> and <strong>TagReadWithInterval</strong>.
In the methods of the cited paper they say:</p>

<blockquote>
  <p>Reads that mapped to intronic or exonic regions of genes as per the GENCODE gene annotation were recorded. </p>
</blockquote>

<p>I think that in this case the tool to use should be <strong>TagReadWithInterval</strong> since the other one should consider only exons.</p>

<p>I cannot find any other documentation about the tools. Do you know/already encountered this problem?</p>

<scrnaseq><gene>
TagReadWithGene missing when using latest version of Drop-seq_tools
# TagReadWithGene missing when using latest version of Drop-seq_tools

(Asked by: username_0 on 2018-09-26)

I am using [Drop-seq\_tools](http://mccarrolllab.org/dropseq/) to analyze scRNA-seq in a similar way of [this paper](https://www.ncbi.nlm.nih.gov/pubmed/29227469). I am using the [same data (GSE97930)](https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE97930) to get used to Drop-seq\_tools.

On the GEO repo the authors provide the relevant code ([GSE97930\_README.txt](https://www.ncbi.nlm.nih.gov/geo/download/?acc=GSE97930&format=file&file=GSE97930%5FREADME%2Etxt)). However, one tool used in the script is missing: **TagReadWithGene**.

The latest version of Drop-seq\_tools does not have such method (as it should be provided by this library), and there is no version history for the whole package, so I cannot download previous versions.

The best matches for the missing method are **TagReadWithGeneExon** and **TagReadWithInterval**.
In the methods of the cited paper they say:

> Reads that mapped to intronic or exonic regions of genes as per the GENCODE gene annotation were recorded.

I think that in this case the tool to use should be **TagReadWithInterval** since the other one should consider only exons.

I cannot find any other documentation about the tools. Do you know/already encountered this problem?

**Tags:** scrnaseq, gene

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## 1 answers

### Answer by username_0 on 2018-09-27. Score: 1 | Accepted answer

As per [this response](https://github.com/broadinstitute/Drop-seq/issues/38#issuecomment-424833407) from Drop-seq\_tools team, at the moment intronic regions cannot be annotated and **TagReadWithGeneExon** should be used instead.

However, in the version of the [public repository](https://github.com/broadinstitute/Drop-seq):

> TagReadWithGeneExonFunction is the old code, for people who want the more simple tagging methodology and rely on it for 3rd party tools, and TagReadWithGeneFunction, which for your purposes replaces TagReadWithGeneExon. [...] You’ll see additional options to extract expression for CODING, UTR, INTRONIC reads [...]


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