[ensembl-dev] Question regarding transcript location data

[Duarte Molha]

In some on my transcript IDS, they have a perfectly correct genomic position in UCSC

As an example, the NM ID - NM_001164277

Has a valid genomic location in UCSC:

http://genome.ucsc.edu/cgi-bin/hgTracks?hgHubConnect.destUrl=..%2Fcgi-bin%2FhgTracks&clade=mammal&org=Human&db=hg19&position=NM_001164277&hgt.suggest=&hgt.suggestTrack=knownGene&Submit=submit&hgsid=279134705

and in ENSEMBL there is no genomic position info... only the patch ID

http://www.ensembl.org/Homo_sapiens/Search/Details?species=Homo_sapiens;idx=Gene;end=1;q=NM_001164277

So, what ideally what I would need is a way of converting the patch ID into a valid chromosome number.

IS there an easy way of doing this?

Best regards

Duarte


From: dev-bounces at ensembl.org [mailto:dev-bounces at ensembl.org] On Behalf Of Duarte Molha
Sent: 20 June 2012 09:20
To: Ensembl developers list
Subject: [ensembl-dev] Question regarding transcript location data

Dear developers

I have a script that retrieves intron and exon information from an input NM ID. It is working pretty well but I have stumbled on a few NM iDS and I would like to know what I can to correct the behaviour of the script.

As an example if I input this ID:

NM_173471

My script ouputs:

INPUT_ID            CHR                                        start                       end                        ENST_ID                               EXON_ID                             strand
NM_173471       chrHG991_PATCH              66119285            66119659             ENST00000566782            ENSE00002619671 0         +1
NM_173471       chrHG991_PATCH              66298434            66298819             ENST00000566782            ENSE00002619173 0         +1
... <abbreviated>

However what I would have liked to have been outputted was the correct genomic location of this transcript... in this case chr3.
Can you tell me how I can change by script so that it gets the correct chr location instead of this PATCH ids?

Basically I would have wanted the script to have outputted the exon/intron data from the first entry on this link:

http://www.ensembl.org/Homo_sapiens/Search/Details?species=Homo_sapiens;idx=Transcript;end=2;q=NM_173471


Best regards,

Duarte Molha

-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://mail.ensembl.org/pipermail/dev_ensembl.org/attachments/20120620/40dc6386/attachment.html>