I have some RNA-seq data from a stranded paired end library prep, with dUTP and UDG preparation, so the orientation should be RF (confirmed with sequencing provider). I assembled the reads with Trinity, specifying RF for the strandedness, and I am mapping the reads to the transcripts with bwa-mem (I am aware bowtie2 or STAR might be better for this, but bwa is what I presently have installed, so just using it to check).
In the bwa output, I see lines
# candidate unique pairs for (FF, FR, RF, RR): (0, 5372, 2, 0), which seems to contradict the expected orientation. Is there a reason that this is expected, or does it indicate a problem?