[maker-devel] Help with updating an annotation

[Saad Arif]

Thank you for the response. I still have one question though, with these options:

est_GFF=cufflinksout.GFF

modle_GFF= ensembl reference.GFF

What happens to cufflinks assembled transcripts that are not confined to current gene loci (i.e. novel genes in cufflinks ouput)? Would i have to prepare ab initio gene predictions for each of these predicted 'new' genes? 
Is there a simple way to combine adding (new genes) and improving of an existing annotation?

Any feedback on this would be greatly appreciated.

saad

On 13 Jun 2014, at 17:59, Carson Holt wrote:

> Use the cufflinks instead of the tophat features (tophat tends to be
> really noisy).  Give the existing models to model_gff (they will then
> always be kept unless something better is found).  There is no option to
> keep models and then just add isoforms.  The model_gff input will either
> be kept as is (unchanged), or replaced with an updated model suggested by
> the evidence (the updated model may contain multiple isoforms though), and
> map_forward=1 can be used to pull names forward from the old model onto
> the new models.
> 
> Thansk,
> Carson
> 
> 
> On 6/13/14, 5:03 AM, "Saad Arif" <saad.arif at tuebingen.mpg.de> wrote:
> 
>> Dear All,
>> 
>> I would like to use Maker pipeline  to expand a current annotation (new
>> isoforms and novel genes with respect to current annotation) and was
>> wondering if anyone had experience with this and or suggestions to my
>> questions.
>> 
>> Briefly:
>> 
>> I have tophat splice junctions from RNAseq data or alternatively
>> cufflinks generated transcript models (fasts format) that i want to use
>> as my new data (est_gff or est).
>> 
>> I want to provide the current Ensembl annotation for gene prediction but
>> i want this annotation to remain unchanged. Hence, i’m not sure if i
>> should provide this annotation as pred_gff
>> or model_gff. Can the model_gff be used for gene prediction or is this
>> just a subset of pred_gff that remain unaltered? Can we provide the same
>> annotation for both options (pred_ and mod_gff)?
>> 
>> 
>> 
>> Importantly, my main goal is to use the new RNAseq data to add more
>> isoforms and (any) novel genes to the existing Ensembl annotation. Any
>> thoughts or suggestions on how to go about  this would be  sincerely
>> appreciated.
>> 
>> 
>> Thanks in advance,
>> saad
>> 
>> 
>> 
>> 
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> 
>