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

[Carson Holt]

Hi Mark,

MAKER will do this.  Currently it is a two step process, in the next MAKER release this will be just one step.  Just supply transcripts from the old assembly as ESTs to MAKER, then set the predictor to est2genome (turn repeatmasking options off by setting them to empty values).  This will map everything forward onto the new assembly.  MAKER at first will destroy the old names because it thinks these are ESTs, so it doesn't give name preservation a priority.  Pulling the old names forward is very easy though with just a second step.  Take the final MAKER output GFF3 file filter it for the source tag est2genome (cat output.gff | grep -P "\test2genome\t" > new.gff).  Then use this GFF3 file as input for the pred_gff option  in MAKER, and set the predictor to pred_gff.  This will map the names forward in the final GFF3 file.

Thanks,
Carson


On 12/4/09 12:55 PM, "Dave Clements, GMOD Help Desk" <help at gmod.org> 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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