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