Ucsc: Which Gene Name Annotation Are You Using?
1
1
Entering edit mode
11.4 years ago

Hi,

I'm doing a locus zoom and I'm wondering which gene annotation to use. In UCSC, you have UCSC, ENCODE/GENCODE and RefSeq genes. So which ones is the "better".

Thanks

ucsc gene annotation • 3.0k views
ADD COMMENT
3
Entering edit mode
11.4 years ago
tayebwajb ▴ 120

I think it depends on which level you are interested in, i.e., genomic or transcriptome. I would use UCSC known genes for the former and GENCODE for the latter. I prefer to use UCSC known genes. I recently was doing structural variant analysis and I found that the breakpoint I obtained in the STAT6 gene was outside the coordinates of the RefSeq genes but within the STAT6 UCSC known gene. This got me confused at first because I thought that the breakpoint was probably in a region where two contigs overlap in the genome assembly, with no annotation in that region.

Apparently, GENCODE v15 contains the most comprehensive functional annotation for the complete human genome. https://gencodegenes.wordpress.com/2013/05/21/gencode-v15-a-complete-firstpass-manual-annotation-of-the-human-genome/

ADD COMMENT

Login before adding your answer.

Traffic: 1305 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6