Dear all, Today I used Tophat to map the reads from RNA-Seq, and had a look at the results using "visaulization" function. In some regions I can see splice junctions calculated by Tophat, but I don't see any reads mapping to this region. Is this a bit strange? I thought "splice junction" is calculated from the mapped reads. However, I think cufflinks only uses "accepted hits" as input, maybe it is not a big problem that "splice junction' is not accurate. Am I right? Was there something wrong when I mapped my reads with tophat? Hope you can help me figure it out. Looking forward to hearing from you. Jiwen
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