I am a newbie to RNA Seq analysis and Galaxy. I was trying to calculate the mean inner distance between mate pairs for Tophat2 but when I run the picard tool on the BWA file (paired end files aligned with reference genome), it results in empty files! Not sure what's happening. I tried few different BWA files but all give the same result.
Also, how do I get the information for Std. Dev for Distance between Mate Pairs?
I would really appreciate the inputs from experienced users.