Hi Martin,
You're right. Currently, this feature isn't implemented (at least not in this manner, in salmon). In alignment-based salmon, orphaned reads are already handled by the model. What I mean by this is that if you have a paired-end read library (say, library type `IU` --- unstranded reads facing toward each other), and some reads are orphaned, either during the QC step or during alignment, but the remaining read has a valid SAM/BAM record in the output, these reads will be appropriately considered during quantification.
For "read-based" salmon, the situation is different. Currently, it is expected that, if the library is paired-end, then both pairs will be present in each read in the input. Further, it is assumed that both reads will map to the same contig in order to generate a valid "alignment". There are two ways to relax this requirement. The first is to allow the orphaning of reads during the mapping phase in read-based salmon. This would still require there to be two reads present for every input fragment, but would allow orphaned mappings if it's the case that no concordant mappings exist for the pair. The second way to relax this requirement is to have something like what is mentioned above, where the paired-end and orphaned reads are separated into different input files prior to running salmon. Then, each can be quantified according to its own, expected, library type, but both libraries are considered during quantification. I'd like to implement (at least) one of these --- but I'm not sure which would be most useful.
--Rob
First, let me say that there is a plan to implement this in salmon.