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

[Carson Holt]

1. I'm wondering if MAKER will take into account both types of evidence?

Yes.

2. Would it be better to merge both PASA and cufflinks gff3s using
gff3_merge? 

You can provide them as a comma separated list of files to the est_gff=
option, or you can merge them using the gff3_merge script that comes with
MAKER.

Unfortunately I have no one best option for which evidence types to include.
Every evidence type can contribute in it's own way to the final results.
When you test using different evidence types, try running on a single large
contig and manually view the results in a browser.

Thanks,
Carson


From:  Selene Lizbeth Fernandez Valverde <uqslizbe at uq.edu.au>
Date:  Thursday, September 5, 2013 3:30 AM
To:  <maker-devel at yandell-lab.org>
Subject:  [maker-devel] Maker: Question on using both Trinity and Cufflinks

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

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