How to download all human canonical transcript IDs from Ensembl version 75, via BioMart?

[Jinghua Frank Feng]

Hello,

I think I know how to download all human transcript IDs from Ensembl version 75, via BioMart. But How can I download only the IDs of canonical transcript? Thanks.

Regards,

Frank

[Thomas Maurel]

Dear Frank,

I am afraid that the canonical transcripts are not available in the Ensembl Gene mart at the moment.

Alternatively, you can retrieve this information using the Ensembl perl API:

1) Get our ensembl perl API on branch 75 from github: “git clone -b release/75 https://github.com/Ensembl/ensembl”

2) Follow the installation documentation: http://www.ensembl.org/info/docs/api/api_installation.html

3) Run the following script:

use strict;
use warnings;
 
use Bio::EnsEMBL::Registry;
my $reg = "Bio::EnsEMBL::Registry";
 
$reg->load_registry_from_db(
   -host => 'ensembldb.ensembl.org',
   -user => ‘anonymous',
   -dbname  => 'homo_sapiens_core_75_37'
);
 
open(OUTFILE, ">human_canonical_transcripts_v75.fa");
 
my $gene_adaptor = $reg->get_adaptor('human', 'core', 'gene');
my @genes = @{$gene_adaptor->fetch_all};
 
while(my $gene = shift @genes) {
  print
    (OUTFILE
        $gene->canonical_transcript->stable_id, ".", $gene->canonical_transcript->version, "\n");
}

If you have any questions regarding the ensembl perl API, please email: help...@ensembl.org

Hope this helps,
Thomas

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Thomas Maurel
Bioinformatician - Ensembl Production Team
European Bioinformatics Institute (EMBL-EBI)
European Molecular Biology Laboratory
Wellcome Trust Genome Campus
Hinxton
Cambridge CB10 1SD
United Kingdom

[Jinghua Frank Feng]

Thank you very much, Thomas. It worked perfectly!

Regards,

Frank