I tried the tool RSeQC infer_experiment.py on my RNAseq bacterial data. I know that my data is reverse stranded but I get the following output :
This is PairEnd Data Fraction of reads failed to determine: 0.0693 Fraction of reads explained by "1++,1--,2+-,2-+": 0.3577 Fraction of reads explained by "1+-,1-+,2++,2--": 0.5730
With the doc of RSeQC we would have expected that we obtain like 0.99 for the "1+-,1-+,2++,2--" because it is reverse stranded, or 0.5/0.5 if it wasn't stranded. But we obtain a strange middle ground.
Do you have any idea of what is happening with the data ?