Answers.Body: <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>
  
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Answers.CreationDate: 2018-09-27T01:30:12.030Z
Answers.LastActivityDate: 2018-09-27T01:30:12.030Z
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Body: <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>
  
Tags: <scrnaseq><gene>
Title: TagReadWithGene missing when using latest version of Drop-seq_tools
ThreadText: # 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
  
  
  ---
  
  ## 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 [...]
  
  
  ---
  
  