I believe a similar question has been asked before (Question: Is Star Managing Strand-Specific Data ? ), but in the answer to that, it was mentioned that we don't need to do anything extra in STAR alignment if we have strand-aware RNA-seq data. But at another place (Are any additional parameters for STAR to hand the stranded RNA-Seq data?), the author of STAR mentions that presently STAR doesn't use strand information for mapping, and that if we use a certain option (--quantMode), it provides output for 3 kinds of strandedness).
So which is it? Does STAR perform strand-aware mapping, which we can use downstream to get antisense transcripts, or if not, then what is the best way to achieve that? I am working with Tru-Seq Stranded Total RNA library, which apparently maps to the opposite strand of the genome (opposite to what you would normally expect).
I am primarily interested in finding novel non-coding transcripts in my data