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

[Mohamed Amine Chebbi]

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 
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://yandell-lab.org/pipermail/maker-devel_yandell-lab.org/attachments/20161026/a60b27ab/attachment-0002.html>
-------------- next part --------------
A non-text attachment was scrubbed...
Name: AED-Graph.pdf
Type: application/pdf
Size: 5328 bytes
Desc: not available
URL: <http://yandell-lab.org/pipermail/maker-devel_yandell-lab.org/attachments/20161026/a60b27ab/attachment-0002.pdf>