Question: Where/how can I download all coding sequences ( CDS ) of human genome?
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gravatar for jamesxli2007
4.7 years ago by
jamesxli200710
Canada
jamesxli200710 wrote:

As the title says, I would like to download all known CDS sequences of human genome with transcript id and exon compositions to my desktop computer for analysis. I tried to get it from BioMart on ensemble.org, it worked for small queries, but my query to load all data always times out. 

thanks

James

rna-seq sequence • 2.8k views
ADD COMMENTlink modified 4.7 years ago by cbio450 • written 4.7 years ago by jamesxli200710

Over here

If you know perl, and use Linux,this will help as well.

They don't have transcript IDs but they have the gene ids, gene names, genome accession number, and coding sequence positions. Don't think they keep the UTRs. There's a unique CCDS id for each.

ADD REPLYlink modified 2.1 years ago by RamRS30k • written 4.7 years ago by anp375170
0
gravatar for cbio
4.7 years ago by
cbio450
cbio450 wrote:

You can find this pretty easily on the UCSC Table Browser.

ADD COMMENTlink modified 2.1 years ago by RamRS30k • written 4.7 years ago by cbio450
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