Hi all,
I am working on RNA-seq using TopHat/Cufflink/Cuffdiff for differential
gene expression and new gene discovery ( this is what I am interested in).
 However, I found many genes that are repeated in the Cuffdiff's ouput.
These are the same genes and at the exact the same locus. There should be
only one gene for 1 line. Something like this:
   *Genes* *Locus* *Status* *q1* *q2* *Log2 Folg change* *Significance*  *
Lnp* *2:74517521-74584544* *OK* *8.91501* *85.2735* *3.25779* *   yes*  *Lnp
* *2:74517521-74584544* *OK* *12.0044* *171.352* *3.83533* *   yes*

If I re-run the Cuffdiff for differential gene expression only ( No gene
discovery), the problem is fixed. Anyone knows how o explain and fix this?
Thank you so much
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