Hello, Sir,
UCSC human refseq exon database has ~248,000 exons, but when I extract from
the table browser, the number is more than 500,000 exons.
Can you explain it for me?
I have tried to find the answer from FAQ, I am confused now. I really need
your help.
I want to get the exon and intron genome information, the formate like this.
Chr number Gene name TSS TTS
exon start position exon end position
Chr1 VDR 98793749
9879374 9879374 9879390
..........
..........
Chr number Gene name TSS
TTS intron start position intron end position
Chr1 VDR 98793749
9879374 9879445 9879489
Thanks very much for your kind help.
Your Sincerely.
Joshua.
Hello, Sir,
> UCSC human refseq exon database has ~248,000 exons, but when I extract from
> the table browser, the number is more than 500,000 exons.
> Can you explain it for me?
> I have tried to find the answer from FAQ, I am confused now. I really need
> your help.
> I want to get the exon and intron genome information, the formate like
> this.
>
> Chr number Gene name TSS TTS
> exon start position exon end position
> Chr1 VDR 98793749
> 9879374 9879374 9879390
> ..........
> ..........
>
> Chr number Gene name TSS
> TTS intron start position intron end position
> Chr1 VDR 98793749
> 9879374 9879445 9879489
>
> Thanks very much for your kind help.
>
> On Thu, Nov 11, 2010 at 6:10 AM, qcshare <[email protected]> wrote:
>
>> Hello, Sir,
>> I need your help.
>> Now, I want to get the intron genome information, the formate like this.
>>
>> Chr number Gene name TSS TTS start
>> position end position
>>
>> Thanks very much for your kind help.
>>
>> Joshua.
>>
>> On Thu, Nov 11, 2010 at 5:58 AM, Brooke Rhead <[email protected]>wrote:
>>
>>> Hi Joshua,
>>>
>>> Thank you for your question. In order to receive an answer in the
>>> timeliest manner and for the benefit of all of our users, for whom we try to
>>> have the most comprehensive archives, I would appreciate it if you resent
>>> your email to [email protected]. In this way, users with similar
>>> problems will be able to benefit from your question and our answers. Thank
>>> you for your understanding in this matter.
>>>
>>> --
>>> Brooke Rhead
>>> UCSC Genome Bioinformatics Group
>>>
>>>
>>> On 11/10/10 13:30, qcshare wrote:
>>>
>>>> Hello Brooke,
>>>> but I did not find the introns data.
>>>> Could you please point it out for me?
>>>> Thanks.
>>>>
>>>> On Tue, Nov 9, 2010 at 7:08 AM, Brooke Rhead <[email protected]>
>>>> wrote:
>>>>
>>>> Hi Joshua,
>>>>>
>>>>> Gene e
>>>>>
>>>>
>>>>
>>>>
>>>> xon information can also be obtained via the Table Browser. In this
>>>>> case,
>>>>> you will need to choose the "Genes and Gene Prediction Tracks" group,
>>>>> and
>>>>> then choose a gene set to use. To get more information about any of
>>>>> the
>>>>> gene tracks, select the track in the Table Browser, and then hit the
>>>>> "describe table schema" button. Once you have selected a gene track,
>>>>> set
>>>>> the output format to "selected fields from primary and related tables".
>>>>> This will allow you to select only the fields you are interested in.
>>>>>
>>>>> For more general instructions on using the table browser, see:
>>>>>
>>>>> Table Browser User Guide:
>>>>> http://genome.ucsc.edu/goldenPath/help/hgTablesHelp.html
>>>>>
>>>>> Video tutorial:
>>>>> http://www.openhelix.com//cgi/tutorialInfo.cgi?id=28
>>>>> (click the "Launch" online tutorial button)
>>>>>
>>>>> --
>>>>> Brooke Rhead
>>>>> UCSC Genome Bioinformatics Group
>>>>>
>>>>>
>>>>>
>>>>> On 11/08/10 13:26, qcshare wrote:
>>>>>
>>>>> Hello,
>>>>>>
>>>>>>> I want to download exons and introns information from the
>>>>>>>
>>>>>>> UCSC, the format like this:
>>>>>>
>>>>>> Chr Gene name exon start position exon end positon
>>>>>>
>>>>>>> chr1 VDR 82938023
>>>>>>> 829387892
>>>>>>> chr2 COLIA1 78989087 78989298
>>>>>>> .....
>>>>>>> .....
>>>>>>>
>>>>>>> Could you please tell me how can I download these information.
>>>>>>> Thanks very much.
>>>>>>>
>>>>>>> Joshua.
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>> On Wed, Sep 29, 2010 at 1:36 AM, Mary Goldman <[email protected]>
>>>>>>> wrote:
>>>>>>>
>>>>>>> Hi Joshua,
>>>>>>>
>>>>>>>> The easiest way to download all the CpG Islands with their
>>>>>>>> coordinates
>>>>>>>> and
>>>>>>>> names is to use the table browser (
>>>>>>>> http://genome.ucsc.edu/cgi-bin/hgTables). First, select the clade,
>>>>>>>> genome
>>>>>>>> and assembly of interest. Next, select "Regulation" from the group
>>>>>>>> pull-down
>>>>>>>> menu and "CpG Islands" from the track pull-down menu. Select
>>>>>>>> "selected
>>>>>>>> fields from primary and related tables" as the output format, enter
>>>>>>>> a
>>>>>>>> name
>>>>>>>> for the output file if you would like (leave blank to keep output in
>>>>>>>> browser), and click "get output". Select the "chrom", "chromStart",
>>>>>>>> "chromEnd" and "name" check boxes and click "get output".
>>>>>>>>
>>>>>>>> I hope this information is helpful. Please feel free to contact the
>>>>>>>> mail
>>>>>>>> list again if you require further assistance.
>>>>>>>>
>>>>>>>> Best,
>>>>>>>> Mary
>>>>>>>> ------------------
>>>>>>>> Mary Goldman
>>>>>>>> UCSC Bioinformatics Group
>>>>>>>>
>>>>>>>>
>>>>>>>> On 9/27/10 9:07 PM, qcshare wrote:
>>>>>>>>
>>>>>>>> Dear Professor,
>>>>>>>>
>>>>>>>>> I want to download the genome CpG islands information, such as the
>>>>>>>>> number
>>>>>>>>> of
>>>>>>>>> chromosome, start/end position of the CpG islands and CpG islands
>>>>>>>>> ID
>>>>>>>>> numbers, I just found the first three items, but I can not found
>>>>>>>>> the
>>>>>>>>> information of CpG islands ID numbers.
>>>>>>>>> Could you please tell me where can I get this information?
>>>>>>>>>
>>>>>>>>> Thank you very much!
>>>>>>>>>
>>>>>>>>> Your Sincerely!
>>>>>>>>>
>>>>>>>>> Joshua.
>>>>>>>>> _______________________________________________
>>>>>>>>> Genome maillist - [email protected]
>>>>>>>>> https://lists.soe.ucsc.edu/mailman/listinfo/genome
>>>>>>>>>
>>>>>>>>>
>>>>>>>>> _______________________________________________
>>>>>>>>>
>>>>>>>> Genome maillist - [email protected]
>>>>>> https://lists.soe.ucsc.edu/mailman/listinfo/genome
>>>>>>
>>>>>>
>>>>
>>
>
_______________________________________________
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