I'm exploring the results from Cuffdiff:

1. `.gene_differential_expression_testing`
2. `.transcript_differential_expression_testing`

On some genes I see multiple entries in the 2) and with opposite log2 direction as:

```
TMEM51    chr1:15479027-15546974    A    B    OK    0.000151584    0.563561    11.8602
TMEM51    chr1:15479027-15546974    A    B    OK    0.741354       3.92E-05    -14.2062
TMEM51    chr1:15479027-15546974    A    B    OK    2.39194        0.460979    -2.37541
```

Moreover the gene TMEM51 is missing in 1)......is that normal?

In the 2) are these multiple gene names are different isoforms, if yes how to know if the isoform is new or known one?
On your transcripts file, everything should have a TCONS ID, if there are two entries with the same gene name, or gene ID, then chances are they'll have a different TCONS ID, implying they're different isoforms of the gene.

If you're seeing the same gene name in the Genes differential expression file from cuffdiff, then that's more concerning, as everything should be collapsed down to an XLOC ID, or essentially a locus that encapsulates the gene.

If you want to know if it's 'novel' under the tuxedo method of detection, you should look at the class code that it's been given, better yet, load up some of the alignments in IGV and judge for yourself. In my experience, I'd take what cufflinks is calling 'novel' with a bucket of salt.