[maker-devel] Merging 2 annotations

[Anthony Bretaudeau]

Hello,

I am working on the annotation of an insect genome, and I have 2 gff files:
-an automatic annotation (done by another lab, with something else than
maker, ~20000genes)
-a manually curated annotation (with webapollo, ~1500 genes)

From this, I would like to produce a single gff combining the 2. I'd
like to keep all the manually curated models, and only the automatic
ones that have no equivalent in the manually curated gff.

Is it possible to do something like this with maker? I guess I could
play with the model_gff option, but I'm not sure how exactly I could use it.

Thank you for your help
Regards

Anthony

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[Carson Holt]

You can give the manually curate ones to model_gff and the other ones to
pred_gff. Then set keep_preds=1. The model_gff resuls always get kept
even without evidence support, the pred_gff will be kept even without
evidence support because you set keep_preds=1, but model_gff results will
take precedence.

--Carson


On 6/3/14, 2:38 AM, "Anthony Bretaudeau"

[Anthony Bretaudeau]

Thank you, it works fine!
A little question which is related: I set the map_forward option to 1,
but it seems to work only for the model_gff gff. Is there a way to make
it keep the original IDs also for the pred_gff file?
Thank you
Anthony

[Daniel Ence]

Hi Anthony, So I think that the gene ID gets changed in the process of promoting things from pred_gff to gene models. If you know which predictions you want to keep, then you can select those out and pass them to model_gff. 

~Daniel

Daniel Ence

Graduate Student

de...@genetics.utah.edu
Eccles Institute of Human Genetics
University of Utah
15 North 2030 East, Room 2100
Salt Lake City, UT 84112-5330

On Jun 12, 2014, at 7:00 AM, Anthony Bretaudeau <anthony.b...@rennes.inra.fr>

 wrote:

[Anthony Bretaudeau]

Yes, I think that's why the ids get changed.
But I don't know which predictions I want to keep as I'm using maker to only keep the ones that are not equivalent to the models that are in the model_gff.

Anthony

[Carson Holt]

This might be a round about way to get them to have the names unaltered.  Give the pred_gff ones to est_gff.  Still give the model_gff ones to model_gff. Set est2genome=1 and single_exon=1.  Then add this line to the control file est_forward=1.  This is normally used to move transcripts forward onto new assemblies with names being drawn from the alignment, but by telling MAKER that these are ESTs instead of predictions and setting the appropriate values, it will think it's moving transcripts forward, and the final result may be what you want.

--Carson