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<p><i></i> </p>
<p>Dear Allan,</p>
<p>Thanks for your email and for using Ensembl services.<br>
</p>
<p>We have 2 main cases: stand-alone species (for instance all the
plants') and species sharing a "collection DB" - like bacteria.</p>
<p>For the stand-alone species - say plants - the path to the
(release 60) GTF would be<br>
<a class="moz-txt-link-freetext"
href="http://ftp.ensemblgenomes.org/pub/plants/release-60/gtf/">http://ftp.ensemblgenomes.org/pub/plants/release-60/gtf/</a><species>/<br>
where <species> can be found from one of the species
metadata files.</p>
<div class="moz-forward-container">For species belonging to a
collection - say bacteria - the path to the (release 60) GTF would
be<br>
<a class="moz-txt-link-freetext"
href="http://ftp.ensemblgenomes.org/pub/release-60/bacteria/gtf/">http://ftp.ensemblgenomes.org/pub/release-60/bacteria/gtf/</a><collection>/<species>/<br>
Regrettably, there is no trivial way to get the collection the
species belongs to.<br>
One hopefully not-too-cumbersome would be to extract it from the
"core_db" field from the species metadata file.<br>
For instance for "acetobacter_syzygii_gca_002276805", we have core
db "bacteria_60_collection_core_60_113_1", the collection name
would be "bacteria_60_collection"; thus giving
<a class="moz-txt-link-freetext"
href="http://ftp.ensemblgenomes.org/pub/release-60/bacteria/gtf/bacteria_60_collection/acetobacter_syzygii_gca_002276805/">http://ftp.ensemblgenomes.org/pub/release-60/bacteria/gtf/bacteria_60_collection/acetobacter_syzygii_gca_002276805/</a><i><br>
</i></div>
<div class="moz-forward-container"><i><br>
</i></div>
<div class="moz-forward-container">Hope it helps.<br>
Any questions, please do not hesitate to ask.<br>
</div>
<div class="moz-forward-container"><br>
</div>
<div class="moz-forward-container">Kind regards,</div>
<div class="moz-forward-container">Stefano on behalf of the Ensembl
team<i><br>
</i></div>
<div class="moz-forward-container"><i><br>
</i></div>
<div class="moz-cite-prefix">On 10/07/2025 6:49 am, Allan Kamau
wrote:<br>
</div>
<blockquote type="cite"
cite="mid:CAF3N6oQaw4bFC2iW9jFxk+Ht4kpKj3u9VWihSgVeMSkLGBVqrQ@mail.gmail.com">
<meta http-equiv="content-type" content="text/html; charset=UTF-8">
<div dir="ltr">
<div dir="ltr">Greetings,
<div><br>
</div>
<div>Given an entry from one of the species metadata files
such as "<a
href="http://ftp.ensemblgenomes.org/pub/plants/release-60/species_EnsemblPlants.txt"
target="_blank" moz-do-not-send="true">ftp.ensemblgenomes.org/pub/plants/release-60/species_EnsemblPlants.txt</a>"
I would like to determine the ftp path to the "gtf" data of
the given species.
<div><br>
</div>
<div>Is there such a mapping file or mechanism that I can
use?</div>
<div><br>
</div>
<div>Or in short if I have an "assembly" value such as
"ASM16007v2" or and an "assembly_accession" label for
example "GCA_000160075.2" is there a way to determine the
ftp path to the gtf data which is "<a
href="http://tp.ensemblgenomes.org/pub/release-60/bacteria/gtf/bacteria_118_collection/abiotrophia_defectiva_atcc_49176_gca_000160075"
target="_blank" moz-do-not-send="true">tp.ensemblgenomes.org/pub/release-60/bacteria/gtf/bacteria_118_collection/abiotrophia_defectiva_atcc_49176_gca_000160075</a>"
in this case?</div>
<div><br>
</div>
<div>Regards,</div>
<div>- Allan.</div>
</div>
</div>
</div>
<br>
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