cuffdiff results, different cuff id for same locus?

[potato84]

Hi,

I'm very new to RNA-Seq. I just ran cuffdiff for comparing gene expression levels in two conditions.

In the gene_exp.diff file, I found that some CUFF ids have the same locus, although the fpkms are different. I'm just wondering why the same locus will be assigned different CUFF ids, and why the expression level is different?

Thank you very much

Xiaoyu

[potato84]

Does anybody meet the similar problem?

[AndyChung]

I am meeting this problem, but the same loucs didn't effect FPKM value.

[ZZQ]

I found the "locus" column in the cuffdiff output is for the locus, not for the gene. For example, human MIR1227 resides in the intron of PLEKHJ1, but the "locus" column for the two genes is identical. I don't know why but it differs actually.