Hi, I am doing paired end alignment using tophat. Since I'm new to this program, I'm a little confusing about the format of the alignment output: accepted_hits.bam. How can I determine which read end it shows for a mate pair? How can I know the inner distance between the mate pairs? If the 7th column is ‘*’ , does it mean one end aligned but the other end not?
Besides, is it -r option still required for paired end read mapping using Tophat? Though I didn't use this option, I still get the alignment result...
Look forward to your suggestions, and thanks for your help in advance!
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