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

[Carson Holt]

Masking doesn’t just affect the gene models, but also evidence alignment and thus scoring. So merging in this way would not make much sense as the second less masked set would always score better because it has more evidence alignments permitted by the lack of masking (not necessarily real, but drawn in by repeats).

The result would be that any attempt of a merge would almost exclusively result in all genes from the second set always scoring higher.

—Carson



> On Oct 10, 2016, at 3:43 AM, Mohamed Amine CHEBBI <mohamed.amine.chebbi at univ-poitiers.fr> wrote:
> 
> 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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