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?

Question

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.

Answer 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.