Answers.Body: <p>Trinity should be assembling its transcripts in the forward sense direction, so as long as you can be confident in your assembly, you can use the <code>Plus</code> option for the <code>--strand</code> argument.</p>
  <p>More generally, when there are a few options to choose from and you're not sure which one is more appropriate, try running a small subset of the data using all options and look at the results. I find that such a results-based checking can help me more quickly understand my data when the documentation is unclear.</p>
  
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Body: <p>I used Trinity to de-novo assemble my RNA seq raw reads. These reads were generated using a strand-specific method. Now I want to do a BLASTx using Diamond. I am unsure what I should keep under its argument &quot;--strand&quot;. Basically, it has three options:</p>
  <ol>
  <li>Plus - if reads align in the forward sense</li>
  <li>Minus - if read align in the reverse sense</li>
  <li>Both - if you want to align in both ways</li>
  </ol>
  <p>The problem is that I don't know if Trinity preserved my information on strand-specificity when constructing its Transcripts. If it did, I can happily choose Plus, I suppose. Any help would be... helpful.</p>
  
Tags: <rna-seq><blast><transcriptome><strandedness><trinity>
Title: I have assembled raw short RNA-seq reads into Transcripts using Trinity. My raw reads were strand-specific. What should I set "--strand" in Diamond?
ThreadText: # I have assembled raw short RNA-seq reads into Transcripts using Trinity. My raw reads were strand-specific. What should I set "--strand" in Diamond?
  
  (Asked by: username_0 on 2024-07-10)
  
  I used Trinity to de-novo assemble my RNA seq raw reads. These reads were generated using a strand-specific method. Now I want to do a BLASTx using Diamond. I am unsure what I should keep under its argument "--strand". Basically, it has three options:
  
  1. Plus - if reads align in the forward sense
  2. Minus - if read align in the reverse sense
  3. Both - if you want to align in both ways
  
  The problem is that I don't know if Trinity preserved my information on strand-specificity when constructing its Transcripts. If it did, I can happily choose Plus, I suppose. Any help would be... helpful.
  
  **Tags:** rna-seq, blast, transcriptome, strandedness, trinity
  
  
  ---
  
  ## 1 answers
  
  ### Answer by username_1 on 2024-07-11. Score: 1
  
  Trinity should be assembling its transcripts in the forward sense direction, so as long as you can be confident in your assembly, you can use the `Plus` option for the `--strand` argument.
  
  More generally, when there are a few options to choose from and you're not sure which one is more appropriate, try running a small subset of the data using all options and look at the results. I find that such a results-based checking can help me more quickly understand my data when the documentation is unclear.
  
  
  ---
  
  