Hello Wei,

The contents of the reference GTF files (original, before analysis) will probably provide some explanation. My guess is that GTF files have different contents and are not directly comparable - RefSeq with full transcripts and Ensembl with full transcripts + potentially partial predictions and/or predicted splice sites. Alternative versions of each may be available. When possible, you most likely will want to be using a reference GTF file that represents complete transcripts.


I don't know what genome you are using, but you can check the source notes at Ensembl (& NCBI) to find out what each annotation build contains. A raw count on the number of entries in the GTF files can also be a clue - if greatly different, then you very likely have different populations in the two files.

Good luck with your project!

Jen
Galaxy team

On 1/7/13 1:47 PM, Wei Liao wrote:
Hi all,

I am analyzing significant differential expressed genes for a pair of
normal V.S tumor, using Cuffdiff 2.0.2.
I noticed that by using ensemble GTF and refseq GTF, the results showed
a big difference on the number of genes being significant expressed.

For ensemble GTF, there are only 250 genes differential expressed.
But for refseq GTF, there are about 1000 genes.

I am running these data on Galaxy server and with the same workflow.

Can anyone explain what is going on here? so which result should I trust?

Thanks.


--
Wei Liao
Research Scientist,
Brentwood Biomedical Research Institute
16111 Plummer St.
Bldg 7, Rm D-122
North Hills, CA 91343
818-891-7711 ext 7645


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