[maker-devel] Updating Reference Gene Models - Legacy - Strategy

[Alessandro Rossoni]

Dear makers of MAKER,
first of all - thank you for this awesome program! In the context of my 
project, I have been running MAKER on a set of novel genomes and it 
worked very well :)

During the last days, I realized that the reference sequences of species 
A that I have been using as starting point for gene model prediction for 
species B, C and D are a bit flawed. How do I know that? Through 
visualization of novel RNA-Seq data that was mapped to the "old" gene 
models of species A, I came to the conclusion that the "old" gene models 
are not really accurate. In fact, between 52–62% of the reads map within 
annotated exonic regions of the genome and up to 47% map within 
intergenic regions. Intron/Exon boarders are pretty messed up and there 
are a lot more transcribed sequences in species A than previously 
thought.

Hence, I would love to update the gene models of species A including the 
new RNA-Seq evidence and hope to get more accurate gene models out of 
it. The more accurate gene models of species A would be then used to 
predict genes for species B, C and D (which are hopefully going to 
benefit from the more accurate input). However, I there is a little 
understanding issue on how to set the parameters of the maker_opts.ctl.

My plan is to produce new RNA-Seq based gene models for species A using 
Cufflinks, Stringtie, Breaker, Trinity and Velvet. I would pass the 
output to the maker_opts.ctl as:

model_gff=Cufflinks.gff,Stringtie.gff,Breaker.gff,Trinity.gff,Velvet.gff 
#the new gene models
est=Species_A_reference_ests.fasta  #the old/flawed gene models
protein=swissprot.fasta

Question 1: is this correct so far?

But what sequences do I use for training the ab-initio predictors?
snaphmm=
augustus_species=

Question 2: Do I use the "old/flawed" sequences that I know are not 
really good? I am not sure what sequences to use for training.

Any help on this issue would be amazing!
Best,
Ale


-- 
Alessandro W. Rossoni, M.Sc.
Institute for Plant Biochemistry
Heinrich-Heine-University

--
http:///www.plant-biochemistry.hhu.de/
E-Mail:  alessandro.rossoni at hhu-duesseldorf.de