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<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D">Hi Anja,<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D">Thank you so much, I truly appreciate it.<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D">Best wishes,<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D">Dayana<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D"><o:p> </o:p></span></p>
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<p class="MsoNormal"><b><span style="font-size:11.0pt;font-family:"Calibri",sans-serif">From:</span></b><span style="font-size:11.0pt;font-family:"Calibri",sans-serif"> Dev <dev-bounces@ensembl.org>
<b>On Behalf Of </b>Anja Thormann<br>
<b>Sent:</b> Tuesday, 29 October 2019 15:47<br>
<b>To:</b> Ensembl developers list <dev@ensembl.org><br>
<b>Subject:</b> Re: [ensembl-dev] output I get for my input file different when I use the web VEP and command line VEP<o:p></o:p></span></p>
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<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal">Hi Dayana,<o:p></o:p></p>
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<p class="MsoNormal"><o:p> </o:p></p>
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<p class="MsoNormal">you could fetch the XML file from uniprot, e.g. <a href="https://www.uniprot.org/uniprot/Q96MT7.xml">https://www.uniprot.org/uniprot/Q96MT7.xml</a><br>
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Then find the <dbReference> tag with type="ensembl" attribute. The section looks like this:<br>
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<dbReference type="Ensembl" id="ENST00000295868"><br>
<molecule id="Q96MT7-1"/><br>
<property type="protein sequence ID" value="ENSP00000295868"/><br>
<property type="gene ID" value="ENSG00000206530"/><br>
</dbReference><o:p></o:p></p>
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<p class="MsoNormal"><o:p> </o:p></p>
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<p class="MsoNormal">A txt version is also available <a href="https://www.uniprot.org/uniprot/Q96MT7.txt">https://www.uniprot.org/uniprot/Q96MT7.txt</a><o:p></o:p></p>
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<p class="MsoNormal"><o:p> </o:p></p>
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<p class="MsoNormal">Best wishes,<o:p></o:p></p>
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<p class="MsoNormal">Anja<o:p></o:p></p>
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<o:p></o:p></p>
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<p class="MsoNormal">On 29 Oct 2019, at 12:38, Dayana Yahalomi <<a href="mailto:dayana.yahalomi@weizmann.ac.il">dayana.yahalomi@weizmann.ac.il</a>> wrote:<o:p></o:p></p>
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<p class="MsoNormal"><o:p> </o:p></p>
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<p class="MsoNormal"><span lang="en-IL" style="font-size:11.0pt;color:#1F497D">Hi Anja,</span><o:p></o:p></p>
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<p class="MsoNormal"><span lang="en-IL" style="font-size:11.0pt;color:#1F497D">This is great thanks for all the explanations and the examples.</span><o:p></o:p></p>
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<p class="MsoNormal"><span lang="en-IL" style="font-size:11.0pt;color:#1F497D">Now I understand.</span><o:p></o:p></p>
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<p class="MsoNormal"><span lang="en-IL" style="font-size:11.0pt;color:#1F497D">Specifically for me, and maybe others, I do need to know the isoform suffix. Is there a way to know/import for each Ensembl transcript the cross-reference in Uniprot/swissprot including
the isoform suffix?</span><o:p></o:p></p>
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<p class="MsoNormal"><span lang="en-IL" style="font-size:11.0pt;color:#1F497D"> </span><o:p></o:p></p>
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<p class="MsoNormal"><span lang="en-IL" style="font-size:11.0pt;color:#1F497D">Thanks,</span><o:p></o:p></p>
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<p class="MsoNormal"><span lang="en-IL" style="font-size:11.0pt;color:#1F497D">Dayana</span><o:p></o:p></p>
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<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D"> </span><o:p></o:p></p>
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<p class="MsoNormal"><b><span style="font-size:11.0pt;font-family:"Calibri",sans-serif">From:</span></b><span class="apple-converted-space"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif"> </span></span><span style="font-size:11.0pt;font-family:"Calibri",sans-serif">Dev
<<a href="mailto:dev-bounces@ensembl.org">dev-bounces@ensembl.org</a>><span class="apple-converted-space"> </span><b>On Behalf Of<span class="apple-converted-space"> </span></b>Anja Thormann<br>
<b>Sent:</b><span class="apple-converted-space"> </span>Tuesday, 29 October 2019 14:12<br>
<b>To:</b><span class="apple-converted-space"> </span>Ensembl developers list <<a href="mailto:dev@ensembl.org">dev@ensembl.org</a>><br>
<b>Subject:</b><span class="apple-converted-space"> </span>Re: [ensembl-dev] output I get for my input file different when I use the web VEP and command line VEP</span><o:p></o:p></p>
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<p class="MsoNormal"> <o:p></o:p></p>
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<p class="MsoNormal">Hi Dayana,<o:p></o:p></p>
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<p class="MsoNormal"> <o:p></o:p></p>
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<p class="MsoNormal">we import our protein cross-references from UniProt. As part of the import we do alignments to provide identity scores. They can be seen on the website, and are usually 100% or close to.<o:p></o:p></p>
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<p class="MsoNormal"> <o:p></o:p></p>
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<p class="MsoNormal">There can be two different Ensembel proteins sequences pointing to the same swissprot id.<o:p></o:p></p>
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<p class="MsoNormal"> <o:p></o:p></p>
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<p class="MsoNormal">For example:<o:p></o:p></p>
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<p class="MsoNormal"> <o:p></o:p></p>
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<p class="MsoNormal"><a href="https://www.uniprot.org/uniprot/Q96MT7"><span style="color:purple">https://www.uniprot.org/uniprot/Q96MT7</span></a><o:p></o:p></p>
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<p class="MsoNormal"> <o:p></o:p></p>
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<p class="MsoNormal">You can see that UniProt associates both isoforms with one gene, but different proteins. In the source data we see:<o:p></o:p></p>
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<p class="MsoNormal"> <o:p></o:p></p>
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<p class="MsoNormal">DR Ensembl; ENST00000295868; ENSP00000295868; ENSG00000206530. [Q96MT7-1]<o:p></o:p></p>
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<p class="MsoNormal">DR Ensembl; ENST00000393845; ENSP00000377428; ENSG00000206530. [Q96MT7-2]<o:p></o:p></p>
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<p class="MsoNormal"> <o:p></o:p></p>
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<p class="MsoNormal">In Ensembl we see that the isoform suffix is not imported:<o:p></o:p></p>
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<p class="MsoNormal"> <o:p></o:p></p>
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<p class="MsoNormal"><a href="https://www.ensembl.org/Homo_sapiens/Transcript/Similarity?db=core;g=ENSG00000206530;r=3:113362865-113441610;t=ENST00000295868"><span style="color:purple">https://www.ensembl.org/Homo_sapiens/Transcript/Similarity?db=core;g=ENSG00000206530;r=3:113362865-113441610;t=ENST00000295868</span></a><o:p></o:p></p>
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<p class="MsoNormal"> <o:p></o:p></p>
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<p class="MsoNormal"> <o:p></o:p></p>
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<p class="MsoNormal">Please let me know if you have any further questions.<o:p></o:p></p>
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<p class="MsoNormal"> <o:p></o:p></p>
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<p class="MsoNormal">Best wishes,<o:p></o:p></p>
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<p class="MsoNormal">Anja<o:p></o:p></p>
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<p class="MsoNormal"> <o:p></o:p></p>
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<p class="MsoNormal"><br>
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<o:p></o:p></p>
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<p class="MsoNormal">On 29 Oct 2019, at 06:57, Dayana Yahalomi <<a href="mailto:dayana.yahalomi@weizmann.ac.il"><span style="color:purple">dayana.yahalomi@weizmann.ac.il</span></a>> wrote:<o:p></o:p></p>
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<p class="MsoNormal"> <o:p></o:p></p>
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<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D">Hi Anja,</span><o:p></o:p></p>
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<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D">Thanks for the response and the information.</span><o:p></o:p></p>
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<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D">I am so sorry!!! I just noticed that the problem is in my script while parsing the two files.</span><o:p></o:p></p>
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<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D"> </span><o:p></o:p></p>
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<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D">But it was very helpful to find out that the coordinates are for the ENSP.. and not swissprot. Thanks again for this information.</span><o:p></o:p></p>
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<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D"> </span><o:p></o:p></p>
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<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D">I hope it is O.K to bother you with one last question. isn’t the Ensembel protein supposed to be 100% match to the swissprot? Can there be two different Ensembel
proteins sequences, two different ENSP.. id’s (maybe isoforms), pointing to the same swissprot id?</span><o:p></o:p></p>
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<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D"> </span><o:p></o:p></p>
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<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D">All the best,</span><o:p></o:p></p>
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<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D">Dayana</span><o:p></o:p></p>
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<p class="MsoNormal"><b><span style="font-size:11.0pt;font-family:"Calibri",sans-serif">From:</span></b><span class="apple-converted-space"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif"> </span></span><span style="font-size:11.0pt;font-family:"Calibri",sans-serif">Dev
<<a href="mailto:dev-bounces@ensembl.org"><span style="color:purple">dev-bounces@ensembl.org</span></a>><span class="apple-converted-space"> </span><b>On Behalf Of<span class="apple-converted-space"> </span></b>Anja Thormann<br>
<b>Sent:</b><span class="apple-converted-space"> </span>Monday, 28 October 2019 16:19<br>
<b>To:</b><span class="apple-converted-space"> </span>Ensembl developers list <<a href="mailto:dev@ensembl.org"><span style="color:purple">dev@ensembl.org</span></a>><br>
<b>Subject:</b><span class="apple-converted-space"> </span>Re: [ensembl-dev] output I get for my input file different when I use the web VEP and command line VEP</span><o:p></o:p></p>
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<p class="MsoNormal"> <o:p></o:p></p>
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<p class="MsoNormal">Hi Dayana,<o:p></o:p></p>
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<p class="MsoNormal"> <o:p></o:p></p>
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<p class="MsoNormal">thank you for the input file and web tool command line. I annotated your input file with both the web tool and command line VEP option and get for both output files 5519 SWISSPROT annotations if I grep for SWISSPROT. This is not the most
in depth comparison. Could you please point me to some examples where you see a difference between the two annotation options?<o:p></o:p></p>
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<p class="MsoNormal"> <o:p></o:p></p>
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<p class="MsoNormal">The coordinates are always given for the Ensembl protein (ENSP...) which means you cannot use the protein position to look up the position in the SwissProt protein.<o:p></o:p></p>
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<p class="MsoNormal"> <o:p></o:p></p>
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<p class="MsoNormal">However, you shouldn’t see any differences between running with the VEP command line tool or the web online tool.<o:p></o:p></p>
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<p class="MsoNormal"> <o:p></o:p></p>
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<p class="MsoNormal">Thanks,<o:p></o:p></p>
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<p class="MsoNormal">Anja<o:p></o:p></p>
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<o:p></o:p></p>
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<p class="MsoNormal">On 28 Oct 2019, at 11:18, Dayana Yahalomi <<a href="mailto:dayana.yahalomi@weizmann.ac.il"><span style="color:purple">dayana.yahalomi@weizmann.ac.il</span></a>> wrote:<o:p></o:p></p>
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<p class="MsoNormal"> <o:p></o:p></p>
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<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D">Hi Anja,</span><o:p></o:p></p>
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<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D">This is the command from the web:</span><o:p></o:p></p>
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<span style="font-size:9.5pt;font-family:"Courier New";color:#666666">./vep --af --appris --biotype --buffer_size 500 --check_existing --distance 5000 --mane --polyphen b --pubmed --regulatory --sift b --species homo_sapiens --symbol --transcript_version --tsl
--uniprot --cache --input_file [input_data] --output_file [output_file]</span><o:p></o:p></p>
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<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D"> </span><o:p></o:p></p>
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<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D">Attached is a vcf file.</span><o:p></o:p></p>
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<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D"> </span><o:p></o:p></p>
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<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D">Thanks,</span><o:p></o:p></p>
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<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D">Dayana</span><o:p></o:p></p>
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<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D"> </span><o:p></o:p></p>
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<p class="MsoNormal"><b><span style="font-size:11.0pt;font-family:"Calibri",sans-serif">From:</span></b><span class="apple-converted-space"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif"> </span></span><span style="font-size:11.0pt;font-family:"Calibri",sans-serif">Dev
<<a href="mailto:dev-bounces@ensembl.org"><span style="color:purple">dev-bounces@ensembl.org</span></a>><span class="apple-converted-space"> </span><b>On Behalf Of<span class="apple-converted-space"> </span></b>Anja Thormann<br>
<b>Sent:</b><span class="apple-converted-space"> </span>Monday, 28 October 2019 11:01<br>
<b>To:</b><span class="apple-converted-space"> </span>Ensembl developers list <<a href="mailto:dev@ensembl.org"><span style="color:purple">dev@ensembl.org</span></a>><br>
<b>Subject:</b><span class="apple-converted-space"> </span>Re: [ensembl-dev] output I get for my input file different when I use the web VEP and command line VEP</span><o:p></o:p></p>
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<p class="MsoNormal"> <o:p></o:p></p>
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<p class="MsoNormal">Dear Dayana,<o:p></o:p></p>
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<p class="MsoNormal"> <o:p></o:p></p>
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<p class="MsoNormal">could you please share which options you are using for the web tool? You can copy the command line equivalent from the job details section. Could you also please share an example for which you are seeing different annotations?<o:p></o:p></p>
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<p class="MsoNormal"> <o:p></o:p></p>
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<p class="MsoNormal">Thank you,<o:p></o:p></p>
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<p class="MsoNormal">Anja<o:p></o:p></p>
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<o:p></o:p></p>
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<p class="MsoNormal">On 28 Oct 2019, at 07:06, Dayana Yahalomi <<a href="mailto:dayana.yahalomi@weizmann.ac.il"><span style="color:purple">dayana.yahalomi@weizmann.ac.il</span></a>> wrote:<o:p></o:p></p>
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<p class="MsoNormal"> <o:p></o:p></p>
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<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif">Dear Ensembl dev,</span><o:p></o:p></p>
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<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif">I have installed the following vep program</span><o:p></o:p></p>
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<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif">Versions:</span><o:p></o:p></p>
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<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif"> ensembl : 98.e98e194</span><o:p></o:p></p>
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<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif"> ensembl-funcgen : 98.36eef94</span><o:p></o:p></p>
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<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif"> ensembl-io : 98.052d23b</span><o:p></o:p></p>
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<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif"> ensembl-variation : 98.7b96c96</span><o:p></o:p></p>
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<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif"> ensembl-vep : 98.2</span><o:p></o:p></p>
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<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif"> </span><o:p></o:p></p>
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<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif">And When I run the following command (offline):</span><o:p></o:p></p>
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<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif">./vep --verbose --species homo_sapiens --assembly GRCh38 --offline --dir_cache=/bio/db/vep98 --input_file ex2.vcf --format vcf --output_file outputfile_uniprot.vep98.2_dayana2.vcf
--vcf --uniprot</span><o:p></o:p></p>
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<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif"> </span><o:p></o:p></p>
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<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif">I don’t get the same results as running the same file example in your web.</span><o:p></o:p></p>
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<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif">I am interested in the protein changes and I look at the SwissProt flag. I used the protein name from SWISSPROT flag and go to the position indicated (Protein_position) and
look if it is correct.</span><o:p></o:p></p>
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<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif">In this case I get fewer protein changes and 30% are incorrect comparing to the web outfile where I get twice as much protein changes and only 10% are incorrect (this is probably
due to different isoforms than the one in Swissprot).</span><o:p></o:p></p>
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<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif">Do you know why I see these differences in the vcf outfile?</span><o:p></o:p></p>
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<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif"> </span><o:p></o:p></p>
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<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif">Thanks in advance,</span><o:p></o:p></p>
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<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif">Dayana</span><o:p></o:p></p>
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<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif"> </span><o:p></o:p></p>
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<p class="MsoNormal"><span style="font-size:9.0pt;font-family:"Helvetica",sans-serif">_______________________________________________<br>
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<p class="MsoNormal"> <o:p></o:p></p>
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<p class="MsoNormal"><ex2m.vcf><span style="font-size:9.0pt;font-family:"Helvetica",sans-serif">_______________________________________________<br>
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Ensembl Blog:<span class="apple-converted-space"> </span></span><a href="http://www.ensembl.info/"><span style="font-size:9.0pt;font-family:"Helvetica",sans-serif;color:purple">http://www.ensembl.info/</span></a><o:p></o:p></p>
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<p class="MsoNormal"> <o:p></o:p></p>
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<p class="MsoNormal"><span style="font-size:9.0pt;font-family:"Helvetica",sans-serif">_______________________________________________<br>
Dev mailing list </span><a href="mailto:Dev@ensembl.org"><span style="font-size:9.0pt;font-family:"Helvetica",sans-serif;color:purple">Dev@ensembl.org</span></a><span style="font-size:9.0pt;font-family:"Helvetica",sans-serif"><br>
Posting guidelines and subscribe/unsubscribe info:<span class="apple-converted-space"> </span></span><a href="https://lists.ensembl.org/mailman/listinfo/dev_ensembl.org"><span style="font-size:9.0pt;font-family:"Helvetica",sans-serif;color:purple">https://lists.ensembl.org/mailman/listinfo/dev_ensembl.org</span></a><span style="font-size:9.0pt;font-family:"Helvetica",sans-serif"><br>
Ensembl Blog:<span class="apple-converted-space"> </span></span><a href="http://www.ensembl.info/"><span style="font-size:9.0pt;font-family:"Helvetica",sans-serif;color:purple">http://www.ensembl.info/</span></a><o:p></o:p></p>
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<p class="MsoNormal"> <o:p></o:p></p>
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<p class="MsoNormal"><span style="font-size:9.0pt;font-family:"Helvetica",sans-serif">_______________________________________________<br>
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Ensembl Blog: <a href="http://www.ensembl.info/">http://www.ensembl.info/</a></span><o:p></o:p></p>
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<p class="MsoNormal"><o:p> </o:p></p>
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