<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>

CC BY-SA 4.0
2018-06-25T13:45:01.087Z
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.
LinuxBlanket
CC BY-SA 4.0
2018-06-25T13:53:37.913Z
Okay, I understood 270 PE reads...
benn
CC BY-SA 4.0
2018-06-25T13:54:20.100Z
Yes, I actually wrote 270 PE reads, my bad.
LinuxBlanket
CC BY-SA 4.0
2018-06-25T13:42:08.387Z
2018-06-25T13:42:08.387Z
benn
<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>

<assembly><transcriptome>
Correct way to assemble reference transcriptome - what's --samples_file option in Trinity?
# 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

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## 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.  

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