[maker-devel] Combining and merging two Maker annotation gff files ?

[Mohamed Amine CHEBBI]

Hi!

I’m using the latest version of Maker2 to annotate an arthropod genome. 
First, I have run RepeatModeler to create rmlib for Maker, then I have 
followed two independent annotation strategies on the same assembly :
1- Passing throw Maker all the repeats collected by RepeatModeler ( 
Identified repeats in the Repbase + Unkown Models).
2- Passing throw Maker only the identified repeats.

Both annotations work successfully. The first annotation gives me 19048  
genes against 22931 done by the second one. Know, I'm seeing for a mean 
to merge the two annotation gff files without _doing a re-annotation 
_and by taking the best and non redundant supported gene models .

So, do you think that configuring  the maker options as below, could 
resolve this issue :
maker_gff=1-mask-all.gff,2-mask-onlyKnown.gff #MAKER derived GFF3 file
#MAKER derived GFF3 file
est_pass=1 #use ESTs in maker_gff: 1 = yes, 0 = no
altest_pass=0 #use alternate organism ESTs in maker_gff: 1 = yes, 0 = no
protein_pass=1 #use protein alignments in maker_gff: 1 = yes, 0 = no
rm_pass=1 #use repeats in maker_gff: 1 = yes, 0 = no
model_pass=0 #use gene models in maker_gff: 1 = yes, 0 = no
pred_pass=1 #use ab-initio predictions in maker_gff: 1 = yes, 0 = no
other_pass=0 #passthrough anyything else in maker_gff: 1 = yes, 0 = no

-- 
Mohamed Amine CHEBBI, PhD Student
Université de Poitiers

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