[BioMart Users] glitch in ID converter ?

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[BioMart Users] glitch in ID converter ?

Brenden Chen
To whom it may concern,

There seems to be a technical glitch in ID converter and I am sending this inquiry to seek assistance/clarification.
I uploaded a list of 30 genes by their HGNC symbols and asked them to be converted into UCSC IDs. After clicking GO, a pop-up window showed up with the conversion results. 
Problems
1. the conversion results in the pop-up window only includes 17 out of the 30 genes submitted.
2. when I clicked on the download data, the downloaded data is incomplete - including some from the 17 genes shown in the pop-up window, and some from the 13 genes NOT shown in the pop-up window.

Attached is the list of genes submitted. Any suggestion as to how I should proceed will be appreciated.

Thank you.
Regards,
Brenden Chen

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biomart gene list.txt (290 bytes) Download Attachment
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Re: [BioMart Users] glitch in ID converter ?

Syed Haider-4
Hi Brenden,

Just ran your 30 genes through ID convertor, and got the results back
(as enclosed). Running length(unique("HGNC symbol")) does show 30
genes. Not sure if you got the same results as enclosed.

Syed



On 14 March 2013 21:51, Brenden Chen <[hidden email]> wrote:

> To whom it may concern,
>
> There seems to be a technical glitch in ID converter and I am sending this
> inquiry to seek assistance/clarification.
> I uploaded a list of 30 genes by their HGNC symbols and asked them to be
> converted into UCSC IDs. After clicking GO, a pop-up window showed up with
> the conversion results.
> Problems
> 1. the conversion results in the pop-up window only includes 17 out of the
> 30 genes submitted.
> 2. when I clicked on the download data, the downloaded data is incomplete -
> including some from the 17 genes shown in the pop-up window, and some from
> the 13 genes NOT shown in the pop-up window.
>
> Attached is the list of genes submitted. Any suggestion as to how I should
> proceed will be appreciated.
>
> Thank you.
> Regards,
> Brenden Chen
>
> _______________________________________________
> Users mailing list
> [hidden email]
> https://lists.biomart.org/mailman/listinfo/users
>

_______________________________________________
Users mailing list
[hidden email]
https://lists.biomart.org/mailman/listinfo/users

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Re: [BioMart Users] glitch in ID converter ?

Brenden Chen
Thanks a lot !! Sorry this is my first time using Biomart.
I also just figured out the output indeed gave me all 30 genes, although I did not expect that the order of the genes would be different.
Any idea why in the BIOmart output some UC IDs are listed as blank? At genome.ucsc site, they all have corresponding UC IDs. I could spot-check all blank IDs this time, but I wonder what if I have a bigger list. Any fix?

Thank you again for the prompt response.
Best,
Brenden

On Thu, Mar 14, 2013 at 7:05 PM, Syed Haider <[hidden email]> wrote:
Hi Brenden,

Just ran your 30 genes through ID convertor, and got the results back
(as enclosed). Running length(unique("HGNC symbol")) does show 30
genes. Not sure if you got the same results as enclosed.

Syed



On 14 March 2013 21:51, Brenden Chen <[hidden email]> wrote:
> To whom it may concern,
>
> There seems to be a technical glitch in ID converter and I am sending this
> inquiry to seek assistance/clarification.
> I uploaded a list of 30 genes by their HGNC symbols and asked them to be
> converted into UCSC IDs. After clicking GO, a pop-up window showed up with
> the conversion results.
> Problems
> 1. the conversion results in the pop-up window only includes 17 out of the
> 30 genes submitted.
> 2. when I clicked on the download data, the downloaded data is incomplete -
> including some from the 17 genes shown in the pop-up window, and some from
> the 13 genes NOT shown in the pop-up window.
>
> Attached is the list of genes submitted. Any suggestion as to how I should
> proceed will be appreciated.
>
> Thank you.
> Regards,
> Brenden Chen
>
> _______________________________________________
> Users mailing list
> [hidden email]
> https://lists.biomart.org/mailman/listinfo/users
>


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https://lists.biomart.org/mailman/listinfo/users
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Re: [BioMart Users] glitch in ID converter ?

Syed Haider-4
The missing UCSC IDs is a question for the data provider i-e Ensembl
BioMart team in this case. Rhoda Kinsella (cc'ed) here can hopefully
help you with this.

Syed



On 14 March 2013 23:21, Brenden Chen <[hidden email]> wrote:

> Thanks a lot !! Sorry this is my first time using Biomart.
> I also just figured out the output indeed gave me all 30 genes, although I
> did not expect that the order of the genes would be different.
> Any idea why in the BIOmart output some UC IDs are listed as blank? At
> genome.ucsc site, they all have corresponding UC IDs. I could spot-check all
> blank IDs this time, but I wonder what if I have a bigger list. Any fix?
>
> Thank you again for the prompt response.
> Best,
> Brenden
>
>
> On Thu, Mar 14, 2013 at 7:05 PM, Syed Haider <[hidden email]> wrote:
>>
>> Hi Brenden,
>>
>> Just ran your 30 genes through ID convertor, and got the results back
>> (as enclosed). Running length(unique("HGNC symbol")) does show 30
>> genes. Not sure if you got the same results as enclosed.
>>
>> Syed
>>
>>
>>
>> On 14 March 2013 21:51, Brenden Chen <[hidden email]> wrote:
>> > To whom it may concern,
>> >
>> > There seems to be a technical glitch in ID converter and I am sending
>> > this
>> > inquiry to seek assistance/clarification.
>> > I uploaded a list of 30 genes by their HGNC symbols and asked them to be
>> > converted into UCSC IDs. After clicking GO, a pop-up window showed up
>> > with
>> > the conversion results.
>> > Problems
>> > 1. the conversion results in the pop-up window only includes 17 out of
>> > the
>> > 30 genes submitted.
>> > 2. when I clicked on the download data, the downloaded data is
>> > incomplete -
>> > including some from the 17 genes shown in the pop-up window, and some
>> > from
>> > the 13 genes NOT shown in the pop-up window.
>> >
>> > Attached is the list of genes submitted. Any suggestion as to how I
>> > should
>> > proceed will be appreciated.
>> >
>> > Thank you.
>> > Regards,
>> > Brenden Chen
>> >
>> > _______________________________________________
>> > Users mailing list
>> > [hidden email]
>> > https://lists.biomart.org/mailman/listinfo/users
>> >
>
>
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Re: [BioMart Users] glitch in ID converter ?

Rhoda Kinsella
Hi Brenden
When you use the Ensembl gene mart and wish to do an "ID conversion", I think it is important to understand what this query is doing. Firstly, for each release, Ensembl maps external reference IDs to our Ensembl gene set (e.g. HGNC and UCSC). This mapping happens approximately 1 to 1.5 months before the release and so you get a snapshot of the mapping that happens at that point in time. UCSC updates nightly for example, so there will be additional information in UCSC that was not present at the time of our mapping.

The second thing to consider is that when you ask  for an "ID conversion", what actually happens is that you ask the Ensembl gene mart (which is ensembl gene centric) for all Ensembl genes that are mapped to the HGNC IDs that you have input and report back any UCSC IDs that are also mapped to that Ensembl gene. Therefore, if there is no mapping to an Ensembl gene, you will get a blank space.

I really hope that helps, but please do get in contact ([hidden email]) if you require more information,
Regards
Rhoda



On 14 Mar 2013, at 23:40, Syed Haider <[hidden email]> wrote:

> The missing UCSC IDs is a question for the data provider i-e Ensembl
> BioMart team in this case. Rhoda Kinsella (cc'ed) here can hopefully
> help you with this.
>
> Syed
>
>
>
> On 14 March 2013 23:21, Brenden Chen <[hidden email]> wrote:
>> Thanks a lot !! Sorry this is my first time using Biomart.
>> I also just figured out the output indeed gave me all 30 genes, although I
>> did not expect that the order of the genes would be different.
>> Any idea why in the BIOmart output some UC IDs are listed as blank? At
>> genome.ucsc site, they all have corresponding UC IDs. I could spot-check all
>> blank IDs this time, but I wonder what if I have a bigger list. Any fix?
>>
>> Thank you again for the prompt response.
>> Best,
>> Brenden
>>
>>
>> On Thu, Mar 14, 2013 at 7:05 PM, Syed Haider <[hidden email]> wrote:
>>>
>>> Hi Brenden,
>>>
>>> Just ran your 30 genes through ID convertor, and got the results back
>>> (as enclosed). Running length(unique("HGNC symbol")) does show 30
>>> genes. Not sure if you got the same results as enclosed.
>>>
>>> Syed
>>>
>>>
>>>
>>> On 14 March 2013 21:51, Brenden Chen <[hidden email]> wrote:
>>>> To whom it may concern,
>>>>
>>>> There seems to be a technical glitch in ID converter and I am sending
>>>> this
>>>> inquiry to seek assistance/clarification.
>>>> I uploaded a list of 30 genes by their HGNC symbols and asked them to be
>>>> converted into UCSC IDs. After clicking GO, a pop-up window showed up
>>>> with
>>>> the conversion results.
>>>> Problems
>>>> 1. the conversion results in the pop-up window only includes 17 out of
>>>> the
>>>> 30 genes submitted.
>>>> 2. when I clicked on the download data, the downloaded data is
>>>> incomplete -
>>>> including some from the 17 genes shown in the pop-up window, and some
>>>> from
>>>> the 13 genes NOT shown in the pop-up window.
>>>>
>>>> Attached is the list of genes submitted. Any suggestion as to how I
>>>> should
>>>> proceed will be appreciated.
>>>>
>>>> Thank you.
>>>> Regards,
>>>> Brenden Chen
>>>>
>>>> _______________________________________________
>>>> Users mailing list
>>>> [hidden email]
>>>> https://lists.biomart.org/mailman/listinfo/users
>>>>
>>
>>

Rhoda Kinsella Ph.D.
Ensembl Production Project Leader,
European Bioinformatics Institute (EMBL-EBI),
Wellcome Trust Genome Campus,
Hinxton,
Cambridge,
CB10 1SD



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