Illumina iGenomes annotation problems

[mrfox]

Hi all,
I am confused by the Illumina iGenomes annotation downloaded from (http://cufflinks.cbcb.umd.edu/igenomes.html).

I downloaded the hg19 annotation under data source "UCSC" and I used the genes.gtf in the annotation folder as the reference to cufflinks/cuffdiff. I found that this annotation is most likely to be the refSeq annotation instead of the UCSC annotation. However, for some genes, such as TP53, the iGenome annotation has 7 transcripts while refSeq has 8 transcripts. Please look at the screenshot: the top panel is the iGenome annotation and the lower is the refSeq annotation. It is easy to see that the last third transcript is not included in iGenome annotation.

I wonder if I misunderstand the iGenome resource.
Could any one help to clarify which annotation(refSeq, genCode, UCSC) is it?

[Dario1984]

The genes.gtf file is a refSeq annotation. The UCSC just refers to it having being downloaded from the UCSC Genome Browser server. It has a different number of transcripts because the iGenomes were made some time ago, but when you go to the genome browser, it automatically uses the current refSeq annotations. Annotations are constantly added and removed from refSeq but there are no version numbers unlike ENSEMBL, so you have no method to understand how much is different.

[mrfox]

Hi Dario1984, thanks for your reply. Cole Trapnell also replied my email. He said that Illumina is still working on this issue and hopefully correct it in the near future.