Multiple "genes" mapping to same locus in cuffdiff

Question

[akainth]

Hi,

After doing cuffmerge of my transcripts files (obtained from cufflink), I ran cuffdiff for my two conditions (CPE and SNE, three replicates each). I got the cuffdiff output file but looking into the gene_exp.diff file I found that multiple "genes" map to exactly same locus with different FPKM. For example as shown below gene id from XLOC_058309 to XLOC_058314 map to chr8:24799827-24941916.

XLOC_058309 XLOC_058309 -   chr8:24799827-24941916  SNE CPE OK  9.24827 1.24035 -2.89844    -0.975675   0.06745 0.392985    no
XLOC_058310 XLOC_058310 -   chr8:24799827-24941916  SNE CPE OK  1.0771  0.335101    -1.68449    -0.386758   0.35795 0.515757    no    
XLOC_058311 XLOC_058311 -   chr8:24799827-24941916  SNE CPE OK  1.92289 0.316673    -2.60221    -0.80857    0.15755 0.449037    no
XLOC_058312 XLOC_058312 -   chr8:24799827-24941916  SNE CPE OK  0.624906    0.0597022   -3.38778    -0.843777   0.1828  0.449037    no
XLOC_058313 XLOC_058313 -   chr8:24799827-24941916  SNE CPE OK  6.3503  1.98556 -1.67728    -0.803834   0.2516  0.464386    no
XLOC_058314 XLOC_058314 -   chr8:24799827-24941916  SNE CPE OK  1.0383  0.211217    -2.29743    -0.981586   0.328   0.499051    no

Is this normal?

[Ram]

Please use the formatting bar (especially the code option) to present your post better. You can use backticks for inline code (`text` becomes text), or select a chunk of text and use the highlighted button to format it as a code block. I've done it for you this time.