I performed my alignment using HISAT2 with strand-specific infromation: --rna-strandness RF. And then I used StringTie to quantify BAMS without --rf tag, now I am concerned if StringTie assumed the libraries to be unstranded. I tried finding some answers on other sources (github), where gpertea (@Github) sort of mentioned that HISAT2 takes care of it; but I didn't find a straight answer.
Also I have other reads aligned with STAR where I didn't use any --rf/--fr information for downstream analysis with StringTie, but the libraries had strand-specific information. Do you suggest I re-run StringTie with appropriate tag for STAR aligned sequences?
Could you help me with it?