text: user4194: I am trying to reproduce the work of this paper
  [1], and I have run StringTie successfully, but after that I have to run Ballgown but could not understand this command:
  >pheno_data = read.csv("geuvadis_phenodata.csv")
  
  Actually, I dont know how to make the .csv file of my samples. What phenotype information should this csv contain?
  I have checked the supplementary data of this research article but didn't find any .csv file.
  How I can make the .csv file for my samples to load the phenotype data for ballgown?
  
  
  Load the phenotype data for the samples. An example file called
    geuvadis_phenodata.csv is included with the data files for this protocol
    (ChrX_data). In general, you will have to create this file yourself. It contains
    information about your RNA sequencing samples, formatted as illustrated in
    this csv (comma-separated values) file. Each sample should be described on
    one row of the file and each column should contain one variable. To read this
    file into R we use the command read.csv. In this file the values are
    separated by commas, but if the file were tabdelimited you could use the
    function read.table.
  
  pheno_data = read.csv("geuvadis_phenodata.csv")
  
  
  
  
  
  Pertea et al, Transcript-level expression analysis of RNA-seq experiments with HISAT, StringTie and Ballgown, Nature Protocols volume 11, pages 1650–1667 (2016) 
  
  
  user6948: You can easily do it via Notepad++ or even Excel. Just don't forget to save the output file as a .csv file (comma-separated value). 
  The info inside should look like (my working example):
  id,state
  lar_control141,control
  lar_control142,control
  lar_control143,control
  lar_probiotic142,probiotic
  lar_probiotic143,probiotic
  lar_probiotic144,probiotic
  lar_probiotic145,probiotic
  lar_probiotic146,probiotic
  
  That should work
  
original_text: 4194: <p>I am trying to reproduce the work of <a href="https://www.nature.com/articles/nprot.2016.095" rel="nofollow noreferrer">this paper</a>
  <a href="https://www.nature.com/articles/nprot.2016.095" rel="nofollow noreferrer">[1]</a>, and I have run StringTie successfully, but after that I have to run Ballgown but could not understand this command:</p>
  
  <pre><code>&gt;pheno_data = read.csv("geuvadis_phenodata.csv")
  </code></pre>
  
  <p>Actually, I dont know how to make the .csv file of my samples. What phenotype information should this csv contain?</p>
  
  <p>I have checked the supplementary data of this research article but didn't find any .csv file.</p>
  
  <p>How I can make the .csv file for my samples to load the phenotype data for ballgown?</p>
  
  <blockquote>
    <ol start="8">
    <li><p>Load the phenotype data for the samples. An example file called
    geuvadis_phenodata.csv is included with the data files for this protocol
    (ChrX_data). In general, you will have to create this file yourself. It contains
    information about your RNA sequencing samples, formatted as illustrated in
    this csv (comma-separated values) file. Each sample should be described on
    one row of the file and each column should contain one variable. To read this
    file into R we use the command read.csv. In this file the values are
    separated by commas, but if the file were tabdelimited you could use the
    function read.table.</p>
    
    <blockquote>
      <p>pheno_data = read.csv("geuvadis_phenodata.csv")</p>
    </blockquote></li>
    </ol>
  </blockquote>
  
  <hr>
  
  <ol>
  <li>Pertea <em>et al</em>, Transcript-level expression analysis of RNA-seq experiments with HISAT, StringTie and Ballgown, <em>Nature Protocols</em> volume 11, pages 1650–1667 (2016) </li>
  </ol>
   6948: <p>You can easily do it via Notepad++ or even Excel. Just don't forget to save the output file as a <code>.csv</code> file (comma-separated value). 
  The info inside should look like (my working example):</p>
  
  <pre><code>id,state
  lar_control141,control
  lar_control142,control
  lar_control143,control
  lar_probiotic142,probiotic
  lar_probiotic143,probiotic
  lar_probiotic144,probiotic
  lar_probiotic145,probiotic
  lar_probiotic146,probiotic
  </code></pre>
  
  <p>That should work</p>
  