Question: Download list of all genes of genome build GRCh38.p0
1
gravatar for akij
3.0 years ago by
akij100
akij100 wrote:

I need to download the list of all genes with their location of genome build GRCh38.p0. Is there any API for this? I just need the gene names and their location something like this

gene name   chromosome  start  end
  ZNF331        19:53569378-53577953
gene • 2.2k views
ADD COMMENTlink modified 3.0 years ago by aka001190 • written 3.0 years ago by akij100

As you are interested in ALL genes, how about trying to download the GTF from the Ensembl FTP release 76, the first with GRCh38?

ADD REPLYlink written 3.0 years ago by Denise CS5.1k

Hi! Thanks a lot. Is there any API where I can input chromosome regions like 19:53569378-53577953 and get a list of Genes within this region for genome build GRCh38.p0?

ADD REPLYlink written 3.0 years ago by akij100

Ensembl REST API.

ADD REPLYlink written 3.0 years ago by genomax87k

Use bioMart or UCSC TableBrowser.

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

ADD REPLYlink written 3.0 years ago by Arup Ghosh2.6k
1
gravatar for aka001
3.0 years ago by
aka001190
Sweden
aka001190 wrote:

You can use Ensembl BioMart to do that.

ADD COMMENTlink modified 3.0 years ago • written 3.0 years ago by aka001190

Could you explain how? I don't see the build version I mentioned there

ADD REPLYlink written 3.0 years ago by akij100

Patches are unlikely to cause major changes in gene information so you should be able to use the current GRCh38 build.

ADD REPLYlink written 3.0 years ago by genomax87k
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