> 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,

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