text: user1637: I have 101 samples from 9 tissues of a nonmodel species, coming either from SRA or sequenced by my lab. I want to generate a reference transcriptome with Trinity for further analysis. In order to do this, I downsampled the reads in order to have 20 to 30M reads for each tissue, for a total of 270M PE reads, which I combined in two files, one for left reads and one for right ones. 
  Now,  I came across the --samples_file flag in Trinity and I'm not sure if I should use it instead of concatenating the transcriptomes. Any help on good practice on this?
  
  user939: --samples_file flag is for DE analysis, you can put info about biological replicates in that file. You say that you want to make a ref transcriptome, so you don't need a samples file for DE analysis.
  Why do you down sample? Are you not afraid you will not have enough reads to have a complete transcriptome now?
  
original_text: 1637: <p>I have 101 samples from 9 tissues of a nonmodel species, coming either from SRA or sequenced by my lab. I want to generate a reference transcriptome with Trinity for further analysis. In order to do this, I downsampled the reads in order to have 20 to 30M reads for each tissue, for a total of 270M PE reads, which I combined in two files, one for left reads and one for right ones. </p>
  
  <p>Now,  I came across the --samples_file flag in Trinity and I'm not sure if I should use it instead of concatenating the transcriptomes. Any help on good practice on this?</p>
   939: <p><code>--samples_file</code> flag is for <a href="https://github.com/trinityrnaseq/trinityrnaseq/wiki/Trinity-Differential-Expression" rel="nofollow noreferrer">DE analysis</a>, you can put info about biological replicates in that file. You say that you want to make a ref transcriptome, so you don't need a samples file for DE analysis.</p>
  
  <p>Why do you down sample? Are you not afraid you will not have enough reads to have a complete transcriptome now?</p>
  