I am newbie for ngs data analysis and so my questions would be very naive. With a lot of struugle I could use infer_experiment.py of rseqc to infer the stranded ness of the single ended publicly availaible dataset data that I was using. The output is displayed as follows:
This is SingleEnd Data Fraction of reads failed to determine:0.0198 Fraction of reads explained by "++,--": 0.4819 Fraction of reads explained by "+-,-+": 0.4982
So can anybody help me in interpreting it that it is stranded or unstranded and how we would guess that? 2. I use hisat2 for alignment and there was an option about strandedness and I used unstranded so it should be fine righht ?