Nick,

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?

Different colors in read data does indicate strandedness; hover over the track and click on the 'Edit Settings' icon (gear) to see/change the sense/anti-sense colors used.

Similar question, is there a way to quantify directionality of the data set?

You can use the Filter SAM tool to filter for mapped strand. Good luck, J.