I am using summarizeOverlaps to count stranded single-end RNA seq data mapped to utr and coding regions of Populus genome. My question is whether summarizeOverlaps can be used for sing-end stranded data generated through dUTP method.  Basically learned from this post http://achri.blogspot.com/2016/02/how-not-to-use-deseq2-for-illumina.html, that you have to invertStrand to get correct strand-specific counts. I appreciate any advice on this matter!

Many Thanks,  Yinan