I know it's a typical question but I couldn't figure it out reading forums and manual. So I have to set this
library-type for TopHat but I don't know how to find what is my library-type! I just checked the
accepted_hits.bam out of TopHat in IGV and
Color aligned by read strand, here is an screenshot but I am not sure if it is telling anything regarding the library type! Any advise on this is appreciated.