Go to Ensembl mart (Human), Select attributes:
- Gene id (which ever system of IDs you have eg Entrez, Ensembl etc),
- HGNC Symbol
Hit Results, then "Export all results" to File ("TSV") with "Unique
results option"
and you have a mapping table of all the genes. No need to send large
number of identifiers to BioMart.
Syed
On 26 February 2013 14:04, Hamid Dolatshad
<[email protected]> wrote:
> Hi Syed
> With my RNAseq data analysis I received a file which looks at expression of
> individual exons of each gene. This means that the geneID are not all
> different (ie not 600k GeneID) but they come as a list with p values and I
> want to be able to convert the list to Gene name. It should eb a simple
> process but I can't seem to be able to find a way of doing it.
>
> Let me know if you can help
> Best
> Hamid
>
> ________________________________________
> From: Syed Haider [[email protected]]
> Sent: 26 February 2013 1:27 PM
> To: Arek Kasprzyk
> Cc: Hamid Dolatshad; [email protected]
> Subject: Re: [BioMart Users] gene ID list limit
>
> Hamid,
>
> just curious - how come you have 600K genes in human, you might want
> to run distinct/unique on your list?
>
> Syed
>
>
> On 26 February 2013 13:06, Arek Kasprzyk <[email protected]> wrote:
>> Hi Hamid,
>> have you tried the ID converter?
>> (http://central.biomart.org/converter/#!/ID_converter/gene_ensembl_config_2)?
>>
>> I dont' think this has a limit.
>>
>> You could also try to split your list into two chunks I suppose
>>
>>
>> a
>>
>>
>>
>> On Tue, Feb 26, 2013 at 12:39 PM, Hamid Dolatshad
>> <[email protected]> wrote:
>>>
>>> Hi
>>> I am trying to convert ensembl gene ID to HGNC symbol and the max that can
>>> be loaded to the site or the ensembl site is 500. my list is 600k list and
>>> it is in a specific order. I was wondering if anyone knows how to quickly
>>> convert the list to the HGNC symbol.
>>> Thanks
>>> Hamid
>>>
>>>
>>>
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>>> https://lists.biomart.org/mailman/listinfo/users
>>>
>>
>>
>>
>>
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