ENSEMBL transcript counts

[Genetics Savvy]

Hi, 

I had downloaded the Ensembl genes data from the UCSC table browser for genome version Hg19. 

Details:

URL: https://genome.ucsc.edu/cgi-bin/hgTables

Clade       - Mammal

Genome   - Human

Assembly: Feb.2009 (GRCh37/hg19)

Group       - Genes and Gene Predictions

Track: GENCODE Gene V24lift37

Table: Comprehensive (wgEncodeGencodeCompV24lift37)

Row Count: 181,716 

Data last updated: 2016-03-02

Can you please let us why the number of records is less than the previous version?

Also, when I looked at: http://www.gencodegenes.org/stats/current_previous_release_compare.html it mentions Ensembl v84 has a total of 199169 transcripts, which is much larger than the number of rows (181,716) in  wgEncodeGencodeCompV24lift37.

Can you please help me understand this difference?

Thanks much in advance!

Savvy

[Luvina Guruvadoo]

Hello Savvy,

Thank you for your email. GENCODE V24lift37 is not a full GENCODE/Ensembl release. It is a projection of the GRCh38 (hg38) V24 release to GRCh37 (hg19).

In order to simply the mapping process, only the annotations on the primary chromosomes are mapped. The annotations on the GRCh38 alt-loci sequences are not included. The process is described here:

http://www.gencodegenes.org/releases/grch37_mapped_releases.html

Note, some GRCh38 annotations end up mapping to GRCh37 alt-loci. Here are the statistics:

all primary
wgEncodeGencodeCompV24lift37 181716 181653
wgEncodeGencodePseudoGeneV19 17149 17125

wgEncodeGencodeCompV19 189020 181236
wgEncodeGencodePseudoGeneV19 16175 15284

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.

Regards,

Luvina

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Luvina Guruvadoo
UCSC Genome Browser
http://genome.ucsc.edu

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[Genetics Savvy]

Okay, thanks Luvina! :)

Thanks,

Savvy