[xiangq]

Hi billstevens,

I only use Ensemble GTF file as annotation and have no idea of other annotation files.
But based on my experience, the cuffdiff will output features using the ID in the annotation file if you give it the GTF file (which is the annotation file and not generated by cuffcompare or cuffmerge).
The output features are all annotated in the GTF, so no novel gene or transcript can be found.
Thanks.

-xiangq

[xiangq]

Thanks for sdriscoll's clarification. It helps.

[xiangq]

As for the CDS output, I double check the data. It seems that the cuffdiff will not output CDS of genes which generate both protein and other non-protein coding RNA.
Anyone can give the reason? Thanks.

[sdriscoll]

I haven't noticed this myself however I haven't paid much attention to the CDS output aside from noting that the file usually has almost as many rows as the gene_exp.diff file.

[billstevens]

So I"m very confused on this GTF format.

From the UCSC wiki, it states "At this time, this genePredToGtf command can provide better GTF files than available from the table browser."

http://genomewiki.ucsc.edu/index.php/Genes_in_gtf_or_gff_format

However, I get outputs from cuffdiff in UNIPROT, RefSeq, UCSC and ENSEMBLE. So that's not a huge deal, I can use DAVID to get all of them. What I am really confused by is this:

One of my CDS is uc010nxq.1. When I search for this on Google, I get this and this

One of these is on chromosome 15 and the other on chromosome X. Please help, I could not be more confused.

Wow, thanks a lot!

I guess we should all be careful when using DAVID then, because it just lets you pick the species, not which genes.

[sdriscoll]

That's why, when I use DAVID, I select OFFICIAL_GENE_SYMBOL as the identifier type for my gene list. To do that I have to have everything in terms of those gene symbols so that's why I've made a point to make sure to get those symbols into the GTF files I use for expression quantification.