[maker-devel] Filter transcripts to improve annotation quality ?

[Michael Campbell]

Hi Amine,

I haven’t seen that pattern in a CFD plot of AED before. Is there a possibility that the x and y axises are swiched in the plot?

Thanks,
Mike
> On Oct 26, 2016, at 9:09 AM, Mohamed Amine Chebbi <mohamed.amine.chebbi at univ-poitiers.fr> wrote:
> 
> Hi !
> I have tried three rounds of annotation in Maker on a non model arthropod genome (1.7Gb) which is an hybrid assembly of Pacbio and illumina reads.
> As suggested in the tutorial, I ran in the first round Maker with repeat masking to generate gene models using transcript (Trinity assembly) and protein (swissprot) evidence. Then Maker models were used twice in a bootstrap fashion to retrain SNAP.  
> The number of genes drops from 29207 in the round 1 to 22547 in the round 2 then increases slightly to 22931 in the round 3.
> 
> However, the AED profile (attached) don't seem to be satisfactory.
> So I wonder if you could let me a good strategy to improve the annotation quality. Do you think that filtering good transcripts could improve results. If yes , which criteria should be taken into account ?
> Thank you.
> 
> Best;
> Amine
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