Thanks for the awesome and full-featured mapper!
I have a question regarding transcriptome BAMs. I am doing bulk RNAseq on bacteria and feeding STAR's transcriptome BAM into Salmon.
Because of bacteria's polycistronic mRNA I'd like to keep orphan read mappings in the transcriptome BAM, i.e. each read of a mate pair could somewhat often map to different but adjacent transcripts/genes and thus be considered orphan reads or singly mapped.
As far as I could tell from the documentation keeping orphan reads is not an option for the transcriptome BAM. Is this correct? Would outputting orphan reads in the transcriptome BAM constitute a new feature request?