[maker-devel] keep_preds option?

[Christoph Hahn]

Hello maker users and developers,

I am new to gene prediction and I am trying to use maker 2.25 on a newly 
assembled non-model organisms draft genome. Within maker I use genemark, 
SNAP and Augustus. I have a few questions:

1. I was wondering what the keep_preds option means exactly.

I found two slightly different explanations on the option
#Add unsupported gene prediction to final annotation set (maker2.25)
#Add non-overlapping ab-inito gene prediction to final annotation set 
(found on the net - probably older maker version)

As far as I understood keep_preds=0 only retains gene models for which 
the ab initio predictions agree. But how many, all three? two of three?
keep_preds=1 instead keeps all gene models regardless if the different 
programs agree, right?

In my case I get substantial differences in the number of gene models 
found between the two settings, while with =1 I get a number that is 
close to what we would expect. How would you interpret that? What would 
you recommend me to do? Obiously =0 is the saver option.

2. I tried to use EST data of an alternative organism in altest= 
(#EST/cDNA sequence file in fasta format from an alternate organism). 
The organism is quite distantly related, but its the closest I have so I 
thought I d give it a shot. I ran maker twice with identical settigs 
expect in altest and est2genome=0/1. The number of genes predicted is 
identical with both approaches, so I am not sure whether or not the EST 
data was actually used or its just to distantly related. Any easy way to 
assess this?

3. I am running maker in several passes and after each pass I am 
training SNAP using the result of the previous pass. Then for every pass 
I run maker from scratch. Would you recommend to supply the gff of the 
previous pass in "#-----Re-annotation Using MAKER Derived GFF3
maker_gff= #re-annotate genome based on this gff3 file", instead?

Thanks in advance for any thoughts/advice on these things! I appreciate 
your help!

much obliged,
Christoph