Hi there,
I apologize if this is covered in documentation or help threads.  searched and it seemed it was not.  I have several illumina rna-seq data sets that "should" be directional.  It seems the directionality is very good, based on the visualization.  First question is; in the visualization window, are the reads color coded by direction, i.e. are orange one direction and blue the other?  If so, it looks like my data is >95% directional.  Similar question, is there a way to quantify directionality of the data set?