List of Genes
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Nefertiti Ojinjideka Hemphill
May 4, 2016, 1:25:13 PM5/4/16
to gen...@soe.ucsc.edu
Hi,
I am trying to compile a list of genes close to snp
rs7310409, and there distances. The directions in the web video list a UCSC gene option that is not available in my browser window. Only an OLD UCSC gene option is available. Please advise on this function.
Thank you!
Nefertiti O Hemphill
Matthew Speir
May 5, 2016, 2:58:58 PM5/5/16
to Nefertiti Ojinjideka Hemphill, gen...@soe.ucsc.edu
Hello Nefertiti,
Thank you for your question about obtaining a list of genes near your SNP.
The instructional video was produced using the hg19 assembly of the human genome assembly, which includes a "UCSC Genes" track. Since the video was produced, we switched our default assembly to the newer hg38 version of the human genome assembly. The hg38 assembly does not include a UCSC Genes track, however, it includes a similar track called "GENCODE v22".
If you want to continue using the hg38 assembly as you are now, then you can just select this "GENCODE v22" from the track drop-down on the Table Browser and the rest of the instructions in the video should remain the same. However, if you want to follow those instructions in the video exactly, then you will need to switch to the hg19 assembly. To do so, in the Table Browser, ensure that you have selected "Mammal" from the "clade" drop-down menu, "Human" from the "genome" drop-down, and "Feb. 2009 (GRCh37/hg19)" from the "assembly" drop-down.
I hope this is helpful. 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 Google Groups forum. If your question includes sensitive data, you may send it instead to genom...@soe.ucsc.edu.
Matthew Speir
UCSC Genome Bioinformatics Group
Thank you for your question about obtaining a list of genes near your SNP.
The instructional video was produced using the hg19 assembly of the human genome assembly, which includes a "UCSC Genes" track. Since the video was produced, we switched our default assembly to the newer hg38 version of the human genome assembly. The hg38 assembly does not include a UCSC Genes track, however, it includes a similar track called "GENCODE v22".
If you want to continue using the hg38 assembly as you are now, then you can just select this "GENCODE v22" from the track drop-down on the Table Browser and the rest of the instructions in the video should remain the same. However, if you want to follow those instructions in the video exactly, then you will need to switch to the hg19 assembly. To do so, in the Table Browser, ensure that you have selected "Mammal" from the "clade" drop-down menu, "Human" from the "genome" drop-down, and "Feb. 2009 (GRCh37/hg19)" from the "assembly" drop-down.
I hope this is helpful. 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 Google Groups forum. If your question includes sensitive data, you may send it instead to genom...@soe.ucsc.edu.
Matthew Speir
UCSC Genome Bioinformatics Group
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