[maker-devel] model_gff question

[Michael Thon]

It seems to have disappeared completely.  I'm running MAKER again now using the tophat alignments that I fed to cufflinks, instead of the cufflinks data.  So far the two models visually checked as missing with the cufflinks data are present as they should be.  I have to wait for the run to finish to get a whole genome count though.  Maybe I need to look more closely at the cufflinks run that I did.  

The RNA-Seq data are from the NCBI SRA and I didn't do anything to clean them up before I ran tophat.


On Oct 2, 2012, at 9:10 AM, Daniel Hughes <dsthughes at gmail.com> wrote:

> 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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> 
> 
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