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Hello Pankaj,<br>
<br>
The GTF does have versions for stable ids, it's just separated out
in to separate fields. These different formats have slightly
different formatting for elements such as the stable ids.<br>
<br>
We do not have a tool to re-version stable ids, however for human
it's just a split of the string on '.' There are three good ways
that should be simple. First, use the GTF file again, this has names
in records. Second, do a split '.' on the stable ids and use it in
biomart as planned. Third, use the REST service lookup endpoint
(<a class="moz-txt-link-freetext" href="http://rest.ensembl.org/documentation/info/lookup">http://rest.ensembl.org/documentation/info/lookup</a>) which takes
versioned stable ids.<br>
<br>
<div class="moz-cite-prefix">On 04/01/17 00:26, Pankaj Agarwal
wrote:<br>
</div>
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<p class="MsoNormal"><span
style="color:#17375E;mso-style-textfill-fill-color:#17375E;mso-style-textfill-fill-alpha:100.0%"><span
style="color:windowtext">Thank you for providing this
clarification. I had just a couple of quick follow up
questions.<o:p></o:p></span></span></p>
<p class="MsoNormal"><span
style="color:#17375E;mso-style-textfill-fill-color:#17375E;mso-style-textfill-fill-alpha:100.0%"><span
style="color:windowtext">These ids came out of
</span></span><span
style="font-size:10.0pt;font-family:"Arial","sans-serif";color:#17375E;mso-style-textfill-fill-color:#17375E;mso-style-textfill-fill-alpha:100.0%;background:white"><span
style="color:windowtext">Ensembl Transcript fasta file (</span></span><span
style="color:#17375E;mso-style-textfill-fill-color:#17375E;mso-style-textfill-fill-alpha:100.0%;border:none
windowtext 1.0pt;padding:0in;background:white"><span
style="color:windowtext">Homo_sapiens.GRCh38.cdna.all.fa)
which I used for the first time in rna-seq data analysis.
Earlier I had been using the GTF file which probably does
not have the version id</span></span><span
style="color:#17375E;mso-style-textfill-fill-color:#17375E;mso-style-textfill-fill-alpha:100.0%"><o:p></o:p></span></p>
<p class="MsoNormal"><span
style="color:#17375E;mso-style-textfill-fill-color:#17375E;mso-style-textfill-fill-alpha:100.0%"><span
style="color:windowtext">1. Is there a function with in
biomart or any Ensembl tool to remove the version numbers
from a list of transcript ids.<o:p></o:p></span></span></p>
<p class="MsoNormal"><span
style="color:#17375E;mso-style-textfill-fill-color:#17375E;mso-style-textfill-fill-alpha:100.0%"><span
style="color:windowtext">and/or<o:p></o:p></span></span></p>
<p class="MsoNormal"><span
style="color:#17375E;mso-style-textfill-fill-color:#17375E;mso-style-textfill-fill-alpha:100.0%"><span
style="color:windowtext">2. Is there a way to get a
mapping from the Transcript IDs to Gene Names that will
circumvent the issue of version id. <o:p></o:p></span></span></p>
<p class="MsoNormal"><span
style="color:#17375E;mso-style-textfill-fill-color:#17375E;mso-style-textfill-fill-alpha:100.0%"><span
style="color:windowtext">Thanks,<o:p></o:p></span></span></p>
<p class="MsoNormal"><span
style="color:#17375E;mso-style-textfill-fill-color:#17375E;mso-style-textfill-fill-alpha:100.0%"><span
style="color:windowtext">- Pankaj<o:p></o:p></span></span></p>
<p class="MsoNormal"><span style="color:#1F497D"><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="color:#1F497D"><o:p> </o:p></span></p>
<div>
<div style="border:none;border-top:solid #B5C4DF
1.0pt;padding:3.0pt 0in 0in 0in">
<p class="MsoNormal"><b><span
style="font-size:10.0pt;font-family:"Tahoma","sans-serif";color:windowtext">From:</span></b><span
style="font-size:10.0pt;font-family:"Tahoma","sans-serif";color:windowtext">
<a class="moz-txt-link-abbreviated" href="mailto:dev-bounces@ensembl.org">dev-bounces@ensembl.org</a> [<a class="moz-txt-link-freetext" href="mailto:dev-bounces@ensembl.org">mailto:dev-bounces@ensembl.org</a>]
<b>On Behalf Of </b>Matthew Laird<br>
<b>Sent:</b> Wednesday, December 21, 2016 8:02 AM<br>
<b>To:</b> Ensembl developers list<br>
<b>Subject:</b> Re: [ensembl-dev] Ensemble GRCh38
Transcript ID<o:p></o:p></span></p>
</div>
</div>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal" style="margin-bottom:12.0pt">Hello Pankaj,<br>
<br>
Those are version numbers, they've been a part of Ensembl
stable ids since the start but not always displayed in every
context, you can read more about the rules for how they're
incremented here:<br>
<br>
<a moz-do-not-send="true"
href="https://urldefense.proofpoint.com/v2/url?u=http-3A__www.ensembl.org_info_genome_stable-5Fids_versions.html&d=CwMD-g&c=imBPVzF25OnBgGmVOlcsiEgHoG1i6YHLR0Sj_gZ4adc&r=IDwpe2wIkw9bdBMqeNsKTRZmbtvkqETUeUnJsNoNd4E&m=3TZBnak0YkbHUaCUhR7sPjdI-kpwbMFVh7Ug_Jtzc8w&s=0dbfmrUnD3j-2gUyaMXfTEYB4CkonFKwa6fSyHhZBR4&e=">http://www.ensembl.org/info/genome/stable_ids/versions.html</a><br>
<br>
Biomart does not accept versioned stable ids in queries, if
you're submitting a batch of stable ids to Biomart you must
ensure they are unversioned.<br>
<br>
Cheers.<o:p></o:p></p>
<div>
<p class="MsoNormal">On 21/12/16 12:52, Pankaj Agarwal wrote:<o:p></o:p></p>
</div>
<blockquote style="margin-top:5.0pt;margin-bottom:5.0pt">
<p class="MsoNormal">Hi,<o:p></o:p></p>
<p class="MsoNormal">The Ensembl Transcript IDs for the GRCh38
version has periods at the end followed by a number. For
ex:<o:p></o:p></p>
<p class="MsoNormal" style="background:white"><span
style="font-size:10.0pt">ENST00000414852.1</span><o:p></o:p></p>
<p class="MsoNormal" style="background:white"><span
style="font-size:10.0pt">ENST00000390399.3</span><o:p></o:p></p>
<p class="MsoNormal" style="background:white"><span
style="font-size:10.0pt">ENST00000610439.4</span><o:p></o:p></p>
<p class="MsoNormal">When I query these in biomart it does not
work. I have remove the period and the following number.<o:p></o:p></p>
<p class="MsoNormal">I was wondering why these were
introduced, what they mean, and how to get these to work
with Biomart.<o:p></o:p></p>
<p class="MsoNormal">Thanks,<o:p></o:p></p>
<p class="MsoNormal">- Pankaj<o:p></o:p></p>
<p class="MsoNormal"><span
style="font-size:7.0pt;font-family:"Verdana","sans-serif"">-----------------------------</span><o:p></o:p></p>
<p class="MsoNormal"><span
style="font-size:7.0pt;font-family:"Verdana","sans-serif"">Pankaj
Agarwal, M.S</span><o:p></o:p></p>
<p class="MsoNormal"><span
style="font-size:7.0pt;font-family:"Verdana","sans-serif"">Bioinformatician</span><o:p></o:p></p>
<p class="MsoNormal"><span
style="font-size:7.0pt;font-family:"Verdana","sans-serif"">Data
Analyst</span><o:p></o:p></p>
<p class="MsoNormal"><span
style="font-size:7.0pt;font-family:"Verdana","sans-serif"">Applied
Therapeutics</span><o:p></o:p></p>
<p class="MsoNormal"><span
style="font-size:7.0pt;font-family:"Verdana","sans-serif"">Div.
of Surgical Sciences</span><o:p></o:p></p>
<p class="MsoNormal"><span
style="font-size:7.0pt;font-family:"Verdana","sans-serif"">Dept.
of Surgery</span><o:p></o:p></p>
<p class="MsoNormal"><span
style="font-size:7.0pt;font-family:"Verdana","sans-serif"">Duke
University</span><o:p></o:p></p>
<p class="MsoNormal"><span
style="font-size:7.0pt;font-family:"Verdana","sans-serif"">M:
919-244-6389</span><o:p></o:p></p>
<p class="MsoNormal"><span
style="font-size:7.0pt;font-family:"Verdana","sans-serif"">O:
919-681-2251</span><o:p></o:p></p>
<p class="MsoNormal"><a moz-do-not-send="true"
href="mailto:p.agarwal@duke.edu"><span
style="font-size:7.0pt;font-family:"Verdana","sans-serif"">p.agarwal@duke.edu</span></a><o:p></o:p></p>
<p class="MsoNormal"> <o:p></o:p></p>
<p class="MsoNormal"><span
style="font-size:12.0pt;font-family:"Times New
Roman","serif""><br>
<br>
<br>
<o:p></o:p></span></p>
<pre>_______________________________________________<o:p></o:p></pre>
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