Hi Katrina,
Thank you very much for your response. The liftOver tool takes only bed
format. I am looking for a GTF format of RNA genes on build hg19. Any
suggestions will be really appreciated.
Best Regards,
Nirmala
------------------------------------------------------------------------------------
Nirmala Akula, MS, PhD
Contractor,
Human Genetics Branch
NIMH/NIH
Blg 35, Rm 1A/205
Bethesda, MD - 20892
Phone# 301-451-4258
-----Original Message-----
From: Katrina Learned [mailto:[email protected]]
Sent: Friday, June 17, 2011 9:06 PM
To: Akula, Nirmala (NIH/NIMH) [C]
Cc: '[email protected]'
Subject: Re: [Genome] FW: hg19 - RNA genes
Hi Nirmala,
To get the Human RNA genes track on hg19, you could do a liftOver from
hg18 to hg19. Please see this information about liftOver (you'll want to
follow the second part about downloading/using the command line version
of the liftOver tool):
http://genome.ucsc.edu/FAQ/FAQdownloads.html#download28
If you are open to using another track, the Gencode Genes has many
non-coding RNAs, and you can filter that track to only show certain
transcript types:
http://genome.ucsc.edu/cgi-bin/hgTrackUi?db=hg19&g=wgEncodeGencode
Another track that might be of interest to you is the sno/miRNA track:
http://genome.ucsc.edu/cgi-bin/hgTrackUi?db=hg19&g=wgRna
Please contact the mail list ([email protected]) again if you have any
further questions.
Katrina Learned
UCSC Genome Bioinformatics Group
Akula, Nirmala (NIH/NIMH) [C] wrote, On 6/17/2011 9:59 AM:
> Dear Pauline,
>
> Below is the response I received from Dr. Eddy. Could you please
> suggest any alternatives to get RNA genes track for hg19?
>
> Thank you very much.
>
> Best Regards,
> Nirmala
>
> ------------------------------------------------------------------------------------
> Nirmala Akula, MS, PhD
> Contractor,
> Human Genetics Branch
> NIMH/NIH
> Blg 35, Rm 1A/205
> Bethesda, MD - 20892
> Phone# 301-451-4258
>
> -----Original Message-----
> From: Eddy, Sean [mailto:[email protected]]
> Sent: Friday, June 17, 2011 12:56 PM
> To: Akula, Nirmala (NIH/NIMH) [C]
> Subject: Re: [Genome] hg19 - RNA genes
>
> I'm sorry, UCSC is mistaken. We did not produce annotation for hg19. Our
> annotation of hg16, the last assembly we annotated (Mar 2004), is here:
> ftp://selab.janelia.org/pub/annotation/human-hg16
>
> Sean
>
> -----
> Sean Eddy | HHMI Janelia Farm Research Campus | http://selab.janelia.org/
>
>
>
>
> On Jun 17, 2011, at 12:35 PM, Akula, Nirmala (NIH/NIMH) [C] wrote:
>
>> Dear Dr. Eddy,
>>
>> I wanted to download RNA genes (hg19) data from UCSC genome browser,
>> but it was unavailable. I e-mailed UCSC bioinformatics team and they asked
>> me to contact you. Could you please let me know when RNA genes track will be
>> available for hg19 build?
>> Thank you very much.
>>
>> Best Regards,
>> Nirmala
>>
>> ------------------------------------------------------------------------------------
>> Nirmala Akula, MS, PhD
>> Contractor,
>> Human Genetics Branch
>> NIMH/NIH
>> Blg 35, Rm 1A/205
>> Bethesda, MD - 20892
>> Phone# 301-451-4258
>>
>> -----Original Message-----
>> From: Pauline Fujita [mailto:[email protected]]
>> Sent: Thursday, June 16, 2011 3:29 PM
>> To: Akula, Nirmala (NIH/NIMH) [C]
>> Cc: '[email protected]'
>> Subject: Re: [Genome] hg19 - RNA genes
>>
>> Hello Nirmala,
>>
>> If you are interested in seeing a version of this track for hg19 you
>> should contact Sean Eddy at Washington University, the original source
>> for the data behind this track.
>>
>> You can read more about this track on its associated description page:
>>
>> http://genome.ucsc.edu/cgi-bin/hgTrackUi?db=hg18&c=chrX&g=rnaGene
>>
>> Best regards,
>>
>> Pauline Fujita
>> UCSC Genome Bioinformatics Group
>> http://genome.ucsc.edu
>>
>>
>> On 06/15/11 14:14, Akula, Nirmala (NIH/NIMH) [C] wrote:
>>> Hi,
>>>
>>> I would like to download Human RNA genes in hg19 assembly.
>>> Could you please let me know when track is going to be available?
>>>
>>> Thank you very much.
>>>
>>> Best Regards,
>>> Nirmala
>>>
>>> ------------------------------------------------------------------------------------
>>> Nirmala Akula, MS, PhD
>>> Contractor,
>>> Human Genetics Branch
>>> NIMH/NIH
>>> Blg 35, Rm 1A/205
>>> Bethesda, MD - 20892
>>> Phone# 301-451-4258
>>>
>>> _______________________________________________
>>> 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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