Q: how to deal with unstranded features?

[qifei9]

Hello,

Thank you very much for this great tool salmon. I currently have a question about how to use it for my data.

First of all, the libtype should be ISR. Then some (not all) of the transcripts that I interested in is unstranded (actually they are on only one strand, but we don't know which one). What should I do for this?

1. assuming they are on + strand, and get the sequences of transcripts. Then run salmon with libtype IU.
2. assuming they are on + strand, and get the sequences of transcripts. Then run salmon with libtype ISR and set --incompatPrior a non-zero value (but what value is suitable?).
3. get 2 sequences for each of those transcripts, one for + strand and one for - strand. Then run salmon with libtype ISR. Finally sum the counts of the 2 sequences.

Which way is more rational, or is there any better way to do?

---

BTW, the changelog of v0.10.2 says:

The new behavior is equivalent to running with the option --incompatPrior 0"

but the doc still says:

Note that Salmon sets this value, by default, to a small but non-zero probability. This means that if an incompatible mapping is the only mapping for a fragment, Salmon will still assign this fragment to the transcript.

Which one the the current default behavior?