[maker-devel] Maker: Question on using both Trinity and Cufflinks

[Selene Lizbeth Fernandez Valverde]

Hi all, 

I'm currently using Maker to reannotate the genome of the marine sponge. We already have a set of Augustus prediction and gene models that I mapped back to the genome using the patched map2assembly script posted on the mailing list, as well as PASA transcripts (based on Trinity assemblies) and cufflinks transcripts. 

I would like to include both Trinity and Cufflinks, as in some cases one outperforms the other. 

I'm currently planning to provide the Trinity/PASA assemblies as fasta to the "est" option and the cufflinks assemblies as gff3 using the "est_gff" option but I'm wondering if MAKER will take into account both types of evidence? Would it be better to merge both PASA and cufflinks gff3s using gff3_merge? 

Thanks in advance for the advice, 

Selene


**est_gff/est --> These are assumed to be correctly assembled and aligned
around splice sites (MAKER uses exonerate to align around splice sites for
ESTs in FASTA files).  MAKER can use them to infer gene models directly
(est2genome option), can use them as support for maintaining predictions,
and can use them to modify structure and add UTR to predictions.  If you
let MAKER try and find alternative splice forms, they will be used to
identify support for splice variants.  How these cluster with other
evidence will help MAKER infer gene boundaries in some cases.  MAKER will
also use splice sites inferred from the ESTs to inform gene predictors
during the prediction step.



Selene Fernandez-Valverde Ph.D.
Postdoctoral Research Fellow
School of Biological Sciences
University of Queensland
St Lucia QLD 4072
Australia
uqslizbe at uq.edu.au

-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://yandell-lab.org/pipermail/maker-devel_yandell-lab.org/attachments/20130905/d23fb088/attachment-0002.html>