<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>

CC BY-SA 4.0
2024-07-11T21:10:26.003Z
2024-07-11T21:10:26.003Z
gringer
<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>

<rna-seq><blast><transcriptome><strandedness><trinity>
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?
# 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

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## 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.


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