<HTML><body>Hi Andy,<BR>
<BR>
Thanks for the reply.<BR>
<BR>
Ah, I see. If I understand correctly, then, the reason why the lifted-over coordinates have the same end position as CHD2 in GRCh37, but a higher start position is because the GRCh38 annotation lacks the upstream putative transcripts (eg ENST00000556722 and ENST00000556930).<BR>
<BR>
Is that correct?<BR>
<BR>
Kind regards,<BR>
Luke<BR>
<BR>
From: <a href="mailto:dev-bounces@ensembl.org">dev-bounces@ensembl.org</a> [mailto:dev-bounces@ensembl.org] On Behalf Of Andrew Yates<BR>
Sent: 22 April 2016 12:28<BR>
To: Ensembl developers list<BR>
Subject: Re: [ensembl-dev] Assembly Coverter incorrect for CHD2 GRCh38 ->GRCh37<BR>
<BR>
Hi Luke,<BR>
<BR>
I think there are a few things going on here to explain that will hopefully resolve your issue.<BR>
<BR>
Firstly the annotation for CHD2 against GRCh38 was from a re-annotation of the genome. That gene was not simply lifted over from the previous assembly but was a fresh call (supported by NM_001271.3 as detailed for the longest transcript from [1]). The line "This gene maps to 93,443,419-93,571,235 in GRCh37 coordinates" is created by lifting over the coordinates from GRCh38 to GRCh37. It is not saying you can find the same gene in GRCh37 at this position. That's why we have the additional link to ENSG00000173575 in GRCh37 to ensure we can send you to the correct locus.<BR>
<BR>
Does that help?<BR>
<BR>
All the best,<BR>
<BR>
Andy<BR>
<BR>
1 - http://www.ensembl.org/Homo_sapiens/Transcript/SupportingEvidence?db=core;g=ENSG00000173575;r=15:92900189-93028005;t=ENST00000394196<BR>
<BR>
------------<BR>
Andrew Yates - Genomics Technology Infrastructure Team Leader<BR>
The European Bioinformatics Institute (EMBL-EBI)<BR>
Wellcome Genome Campus<BR>
Hinxton, Cambridge<BR>
CB10 1SD, United Kingdom<BR>
Tel: +44-(0)1223-492538<BR>
Fax: +44-(0)1223-494468<BR>
Skype: andy.yates.ebi<BR>
<a href="http://www.ebi.ac.uk/" target="_blank">http://www.ebi.ac.uk/</a><BR>
<a href="http://www.ensembl.org/" target="_blank">http://www.ensembl.org/</a><BR>
<BR>
On 22 Apr 2016, at 09:55, Luke Goodsell <Luke.Goodsell@ogt.com> wrote:<BR>
<BR>
Hi,<BR>
<BR>
Are misconversions by the Assembly Converter being fixed?<BR>
<BR>
On the GRCh38 EnsEMBL browser page for CHD2 (http://www.ensembl.org/Homo_sapiens/Gene/Summary?db=core;g=ENSG00000173575), it states “This gene maps to 93,443,419-93,571,235 in GRCh37 coordinates.” However, the GRCh37 page (http://grch37.ensembl.org/Homo_sapiens/Gene/Summary?db=core;g=ENSG00000173575) shows the co-ordinates as “Chromosome 15: 93,426,526-93,571,237”.<BR>
<BR>
These co-ordinates are the same as the “Assembly Converter” conversion, from which I assume the browser takes its data.<BR>
<BR>
Kind regards,<BR>
Luke<BR>
<BR>
<BR>
<BR>
<BR>
Disclaimer<BR>
The information contained in this communication from the sender is confidential. It is intended solely for use by the recipient and others authorized to receive it. If you are not the recipient, you are hereby notified that any disclosure, copying, distribution or taking action in relation of the contents of this information is strictly prohibited and may be unlawful.<BR>
<BR>
This email has been scanned for viruses and malware, and may have been automatically archived by Mimecast Ltd, an innovator in Software as a Service (SaaS) for business. Providing a safer and more useful place for your human generated data. Specializing in; Security, archiving and compliance. To find out more Click Here.<BR>
_______________________________________________<BR>
Dev mailing list Dev@ensembl.org<BR>
Posting guidelines and subscribe/unsubscribe info: http://lists.ensembl.org/mailman/listinfo/dev<BR>
Ensembl Blog: http://www.ensembl.info/<BR>
<br /><br /><p style="font-family: Verdana; font-size:10pt; color:#666666;"><b>Disclaimer</b></p><p style="font-family: Verdana; font-size:8pt; color:#666666;">The information contained in this communication from the sender is confidential. It is intended solely for use by the recipient and others authorized to receive it. If you are not the recipient, you are hereby notified that any disclosure, copying, distribution or taking action in relation of the contents of this information is strictly prohibited and may be unlawful.<br /><br />This email has been scanned for viruses and malware, and may have been automatically archived by <b>Mimecast Ltd</b>, an innovator in Software as a Service (SaaS) for business. Providing a <b>safer</b> and <b>more useful</b> place for your human generated data. Specializing in; Security, archiving and compliance. To find out more <a href="http://www.mimecast.com/products/" target="_blank">Click Here</a>.</p></body></HTML>