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.
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