Answers.Body: <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>
  
Answers.ContentLicense: CC BY-SA 4.0
Answers.CreationDate: 2018-06-25T13:45:01.087Z
Answers.Text: Thanks, it's what I was thinking. // I have 270 million reads, I think it's enough. Using all transcriptomes means having >750 million reads, I don't have the computational resources to assemble it.
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Answers.CreationDate: 2018-06-25T13:53:37.913Z
Answers.Text: Okay, I understood 270 PE reads...
Answers.UserDisplayName: benn
Answers.ContentLicense: CC BY-SA 4.0
Answers.CreationDate: 2018-06-25T13:54:20.100Z
Answers.Text: Yes, I actually wrote 270 PE reads, my bad.
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Answers.CreationDate: 2018-06-25T13:42:08.387Z
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Body: <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>
  
Tags: <assembly><transcriptome>
Title: Correct way to assemble reference transcriptome - what's --samples_file option in Trinity?
ThreadText: # Correct way to assemble reference transcriptome - what's --samples_file option in Trinity?
  
  (Asked by: username_0 on 2018-06-21)
  
  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?
  
  **Tags:** assembly, transcriptome
  
  
  ---
  
  ## 1 answers
  
  ### Answer by username_1 on 2018-06-25. Score: 2 | Accepted answer
  
  `--samples_file` flag is for [DE analysis](https://github.com/trinityrnaseq/trinityrnaseq/wiki/Trinity-Differential-Expression), 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?
  
  > **Comments:**
  > **username_0**: Thanks, it's what I was thinking. // I have 270 million reads, I think it's enough. Using all transcriptomes means having >750 million reads, I don't have the computational resources to assemble it.  
  > **username_1**: Okay, I understood 270 PE reads...  
  > **username_0**: Yes, I actually wrote 270 PE reads, my bad.  
  
  ---
  
  