[Gmod-help] Re: [maker-devel] [Gmod-gbrowse] Massive lift-over of data from mm8 to mm9 - best way

[Mark Yandell]

On Dec 4, 2009, at 12:55 PM, Dave Clements, GMOD Help Desk wrote:

> Hi Mark,
>
> MAKER (see http://gmod.org/wiki/MAKER_Tutorial and
> http://gmod.org/wiki/MAKER - which points you to the main MAKER site)
> supports moving annotation from one assembly to another.  I don't
> remember the details, but if you can't find them, please post to the
> MAKER list (cc'd here).
>
> Dave C.
>
> On Wed, Dec 2, 2009 at 3:39 PM, Wes Barris <wes.barris at csiro.au>  
> wrote:
>> mark meyer wrote:
>>> Hi all,
>>>
>>> We have a massive amount of ChIP-chip, ChIP-seq data that needs to  
>>> be
>>> lifted over to mm9 from mm8.
>>>
>>> A) Is there a way to do this within Gbrowse itself?
>>
>> Not that I am aware of.
>>
>>> B) What is the easiest way to do this?  If Gbrowse can't, can  
>>> someone
>>> recommend a quick way with detailed instructions?  I know that  
>>> UCSC has
>>> a liftover tool, but it seems very slow and can only process one  
>>> file at
>>> a time.
>>
>> I use the UCSC livtover tool quite often.  Why not write a little
>> script to do your work.
>>
>>> We literally have hundreds, if not > 1k, GFF files that need to be
>>> converted.
>>
>> Be carefull when lifting over features with parents.  It is possible
>> to have children lifted over but not the parent.
>>
>>> My guess it would be easiest to do this within Gbrowse itself  
>>> since it
>>> is already databased, but didn't see a quick way to do this.   
>>> Sorry if I
>>> missed something in the documentation.
>>>
>>> Thanks,
>>>
>>> Mark
>>
>>
>> --
>> Wes Barris <wes.barris at csiro.au>
>>
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>
>
>
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