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

[Elyssa Garza]

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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