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

[Dave Clements, GMOD Help Desk]

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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