[maker-devel] model_gff question

[Daniel Hughes]

Did the whole model vanish or just the protein product - contaminated
rnaseq that hasn't been cleaned up enough will regularly cause the later to
become part of a bad utr.

Dan
On Oct 2, 2012 6:01 AM, "Michael Thon" <mike.thon at gmail.com> wrote:

> I looked at two cases in which the model_gff disappeared and they occurred
> in regions where there are multiple overlapping cufflinks features.  One
> model that I'm looking at right now has overlapping protein2genome and a
> SNAP feature overlapping it but it was still not included in the output.
>  it could be a problem in MAKER or it could be a problem with my RNA Seq
> data.  I aligned the RNA Seq data using tophat/cufflinks and converted the
> transcripts.gtf file to gff using  cufflinks2gff3 script.
>
> Is it better to use RNA Seq feature from tophat or cufflinks?
>
>
> On Oct 1, 2012, at 4:01 PM, Carson Holt <carsonhh at gmail.com> wrote:
>
> They can be replaced under two circumstances.
> 1. If you provide two model_gff files (comma separated list), in which
> case MAKER thinks it is merging legacy annotations and will only keep one
> or the other if models overlap.
> 2. If you turn snap, augusutus, genemark, or est2genome on.  MAKER sees
> this as a cue that if these other programs produce a better model, it can
> replace the current model.  If you set map_forward=1, MAKER will conserve
> the name of the previous model (so models change structure but names are
> conserved); otherwise, it gets a new name.  Sometimes groups like to rename
> models every time their is a structural change.  I think you are supposed
> to get the Alias attribute set when you don't get names mapped forward
> though (I can't remember if I added this or just planned on adding the
> Alias mapping though).
>
> MAKER should never drop a model_gff model.  It can only replace it if
> something better comes along, but it should not disappear.
>
> Thanks,
> Carson
>
>
> From: Michael Thon <mike.thon at gmail.com>
> Date: Monday, 1 October, 2012 1:53 AM
> To: <maker-devel at yandell-lab.org>
> Subject: [maker-devel] model_gff question
>
> Under what circumstances will maker not include a gene model from the
> model_gff file in its final output?  It was my understanding from this post:
>  https://groups.google.com/d/topic/maker-devel/Y5jSdZ1Olcc/discussion
>
> That maker will keep or replace models in model_gff and never remove them.
>  I'm reannotating a fungal genome and in model_gff I'm providing the gene
> models originally made by the sequencing center.  I have 12006 models in
> the file I specify in model_gff but maker's final annotation has only 10727
> models in it.
> -Mike
>
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