[maker-devel] First time using maker- Train or not to train?

[Daniel Ence]

Hi Elyssa,

Setting est2genome=1 tells MAKER to promote all of the est2genome alignments to a gene model, which is not what you want for a final gene set. That being said, since your gene models are basically the unmodified alignments, I’m surprised that all of them have an AED of 1, since that means that they’re not supported by any of the evidence (either est or protein).

Did you get gene models from snap or augustus? You can gather those with the fasta_merge script. Those should be a good starting place for training ab initio predictors. Instructions for training snap can be found here:
http://gmod.org/wiki/MAKER_Tutorial#Training_ab_initio_Gene_Predictors

Augustus can also be trained but is much more involved.

~Daniel


Daniel Ence
Graduate Student
Eccles Institute of Human Genetics
University of Utah
15 North 2030 East, Room 2100
Salt Lake City, UT 84112-5330

On Dec 11, 2015, at 10:43 AM, Elyssa Garza <elyssa_garza at yahoo.com<mailto:elyssa_garza at yahoo.com>> wrote:

Hello,

I have recently begun running Maker.  I am currently trying to annotate my Caulanthus Genome (~372Mb); a relative to Arabidopsis.  I am unsure about the parameters I have chosen for my first run in maker, which include:

genome=CAB_assembly.fasta (1044 contigs)
est=Representative_transcript_loci.fasta (assembled transcripts btw 200-20000bp long)
protein=TAIR10pep.fasta (Arabidopsis proteins)
—
Repeat masking
model_org=arabidopsis
rmlib=list of Brassicaceae and common plant repeats
repeat_protein=te_proteins.fasta
Gene Prediction
snaphmm=A.thaliana.hmm
augustus_species=arabidopsis
est2genome=1

I have run a sample file of scaffolds, as well as the entire genome.
In the sample file of scaffolds, I gff3merged the gffs and then ran evaluator.  I noticed that my AED are all 1.  Is this bad?  What should I try next?

I am also unsure on how to train files and if this should be done in my case.

Can anyone advise me on these issues?

-Elyssa
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