After using infer experiment, I get the following type of data:
This is PairEnd Data
Fraction of reads failed to determine: 0.4197
Fraction of reads explained by “1++,1–,2±,2-+”: 0.0028
Fraction of reads explained by “1±,1-+,2++,2–”: 0.5775
This means that is reverse stranded data correct?
Also I am using the latest version of the gtf file, why am I still getting 41% failed to determine?