2
$\begingroup$

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?

Improve this question
$\endgroup$

1 Answer 1

Reset to default
2
$\begingroup$

--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?

Improve this answer
$\endgroup$
3
  • $\begingroup$ 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. $\endgroup$
    – LinuxBlanket
    Jun 25, 2018 at 13:45
  • $\begingroup$ Okay, I understood 270 PE reads... $\endgroup$
    – benn
    Jun 25, 2018 at 13:53
  • $\begingroup$ Yes, I actually wrote 270 PE reads, my bad. $\endgroup$
    – LinuxBlanket
    Jun 25, 2018 at 13:54

Your Answer

By clicking “Post Your Answer”, you agree to our terms of service and acknowledge that you have read and understand our privacy policy and code of conduct.

Not the answer you're looking for? Browse other questions tagged or ask your own question.