Hi Nirmala,
The warning is probably the same reason as this part of the usage statement:
|-gff File is in gff/gtf format. Note that the gff lines are converted
separately. It would be good to have a separate check after this
that the lines that make up a gene model still make a plausible gene
after liftOver|
Most formats that we deal with are line-oriented -- the entire feature
is contained on one line. However, one transcript has many rows in GFF:
one line for the whole thing, a line for each exon, and a line for each
coding portion of an exon (CDS); often a start_codon and stop_codon line
too.
So it's possible that some lines for a gene can be liftOver'd, but not
all; it would be possible for a CDS line to be lifted over, but not the
larger exon that the CDS is a part of. That could cause trouble with
downstream tools.
I think the warning is just a caveat... the output may be fine for the a
user's purposes, it just depends on what doesn't get lifted and what
downstream tools require.
Also see this previous mailing list question for further explanation:
https://lists.soe.ucsc.edu/pipermail/genome/2011-March/025305.html
Please let us know if you have any additional questions: [email protected]
-
Greg Roe
UCSC Genome Bioinformatics Group
On 6/20/11 2:22 PM, Akula, Nirmala (NIH/NIMH) [C] wrote:
> Thank you Greg. When I ran liftOver with the following command:
>
> ./liftOver -gff myfileHg18.gtf hg18ToHg19.over.chain myfileHg19.gtf
> myfileUnmapped.gtf
>
> I got the following warning:
>
> "WARNING: -gff is not recommended"
>
> The output looks fine but is there something I need to look for?
>
> 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: Greg Roe [mailto:[email protected]]
> Sent: Monday, June 20, 2011 4:36 PM
> To: Akula, Nirmala (NIH/NIMH) [C]
> Cc: '[email protected]'
> Subject: Re: [Genome] FW: hg19 - RNA genes
>
> Hi Narmala,
>
> The command line version of liftOver does accept gtf format. You can
> download it for Mac or Linux here: http://hgdownload.cse.ucsc.edu/admin/exe/
>
> Alternatively, you can upload your data as a custom track and use the
> table browser (http://genome.ucsc.edu/cgi-bin/hgTables) to output it as
> bed. Just go the Table Browser and click the "add custom tracks" button,
> add the data as a custom track, and select output format: BED, and
> click get output.
>
> - Greg
>
>
>
> On 6/20/11 11:48 AM, Akula, Nirmala (NIH/NIMH) [C] wrote:
>> 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
>> _______________________________________________
>> Genome maillist - [email protected]
>> https://lists.soe.ucsc.edu/mailman/listinfo/genome
_______________________________________________
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