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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>
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<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"> dev-bounces@ensembl.org [mailto:dev-bounces@ensembl.org]
<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>
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<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 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>
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<p class="MsoNormal">On 21/12/16 12:52, Pankaj Agarwal wrote:<o:p></o:p></p>
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<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 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>
<pre>Dev mailing list <a href="mailto:Dev@ensembl.org">Dev@ensembl.org</a><o:p></o:p></pre>
<pre>Posting guidelines and subscribe/unsubscribe info: <a href="https://urldefense.proofpoint.com/v2/url?u=http-3A__lists.ensembl.org_mailman_listinfo_dev&d=CwMD-g&c=imBPVzF25OnBgGmVOlcsiEgHoG1i6YHLR0Sj_gZ4adc&r=IDwpe2wIkw9bdBMqeNsKTRZmbtvkqETUeUnJsNoNd4E&m=3TZBnak0YkbHUaCUhR7sPjdI-kpwbMFVh7Ug_Jtzc8w&s=DMspTuFLpDSfscMlV8PrB5LcpsM-ijYchewLniAtmn4&e=">http://lists.ensembl.org/mailman/listinfo/dev</a><o:p></o:p></pre>
<pre>Ensembl Blog: <a href="https://urldefense.proofpoint.com/v2/url?u=http-3A__www.ensembl.info_&d=CwMD-g&c=imBPVzF25OnBgGmVOlcsiEgHoG1i6YHLR0Sj_gZ4adc&r=IDwpe2wIkw9bdBMqeNsKTRZmbtvkqETUeUnJsNoNd4E&m=3TZBnak0YkbHUaCUhR7sPjdI-kpwbMFVh7Ug_Jtzc8w&s=oMs4WTlyA3iE4Ie_BDetszY9Q_CzyOS6w_ukqFyp1yY&e=">http://www.ensembl.info/</a><o:p></o:p></pre>
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