[maker-devel] Help with updating an annotation

[Carson Holt]

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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