[maker-devel] Merging gene predictions....

[Gowthaman Ramasamy]

Can i use the following approach Carson?

This is your reply to one of the earlier question:

I've attached a made from scratch drop-in replacement that you can use to do what the old script would have done.  In the current release of MAKER, instead of the gff3_preds2models script users can just give MAKER  a set of predictions in GFF3 format (pred_gff option) and set keep_preds=1 (then leave all other options blank).  The predictions given will the be converted into gene models.

Thanks,
Carson



________________________________________
From: maker-devel-bounces at yandell-lab.org [maker-devel-bounces at yandell-lab.org] On Behalf Of Gowthaman Ramasamy [gowthaman.ramasamy at seattlebiomed.org]
Sent: Thursday, May 24, 2012 12:30 PM
To: Carson Holt; maker-devel at yandell-lab.org
Subject: [maker-devel] Merging gene predictions....

Hi Carson and others,
I am wondering if I can use Maker to merge gene predictions from three gff files. One of the algorithm is 'augustus' which of course i can use it inside Maker. Other two are not part of Maker.

But, in case if I want to pass only the GFFs to Maker and ask it to merge the annotations (when overlap) and pick only annotation that are predicted in 2 out of 3 gffs. Is it possible? I prefer this approach, as we need to run a blast based validation step on predicted features before even try to merge them. Thats another reason why we dont prefer to use the augustus inside maker.

Thanks,
Gowthaman
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