[ensembl-dev] Question regarding transcript location data

Duarte Molha Duarte.Molha at ogt.co.uk
Wed Jun 20 09:48:35 BST 2012

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:


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


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


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:


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:


Best regards,

Duarte Molha

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