Gencode v24 track

[Davide Carnevali]

Hi,
i've downloaded the gencode v24 comprehensive gene annotation dataset (
ftp://ftp.sanger.ac.uk/pub/gencode/Gencode_human/release_24/gencode.v24.annotation.gtf.gz)
and compared it to the gencode v24 dataset from UCSC Table browser
The first has 199215 transcripts, while the one from UCSC has 182435
I tried also to compare  the gencode basic annotation with UCSC gencode v24 track data but here again the 'original' gencode dataset have a different number of transcripts (100972)
Could you explain this? Is there a way to get the same transcript of gencode from UCSC
Table Browser?
Thank you

Best,


--

Davide Carnevali

[Christopher Lee]

Hi Davide,

Thank you for your question about transcript counts from the
GencodeV24 Comprehensive track. The Comprehensive track does not
contain pseudogene annotations, and is likely the reason for the noted
differences with the file provided by Gencode.

You can use the Table Browser to download both the Comprehensive set
and the Pseudogene set and then you should have the same set of
transcripts as those you downloaded directly from
http://www.gencodegenes.org.

We are also going to fix our documentation to more clearly describe
that the Comprehensive track does not include the pseudogene
annotations.

Please let us know if you have any further questions!

Thank you again for your inquiry and using the UCSC Genome Browser. If
you have any further questions, please reply to gen...@soe.ucsc.edu.
All messages sent to that address are archived on a
publicly-accessible forum. If your question includes sensitive data,
you may send it instead to genom...@soe.ucsc.edu.

Want to share the Browser with colleagues?
Host a workshop: http://bit.ly/ucscTraining

Christopher Lee
UCSC Genomics Institute

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[Davide Carnevali]

Got it!

Thank you

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Davide Carnevali