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

[chebbi mohamed amine]

Thank you Carson for your quick response. Sorry, I have another question concerning Augustus Training. You posted previously in the mailing list a link to an explanation of Augustus training steps http://brie4.cshl.edu/pipermail/gmod-help/2012-June/001724.htm l . Unfortunately the link doesn't work anymore. Otherwise could you explain how to filter the gff file produced by the first run of Maker to get best full length ORF as a set of gene models to train Augustus ? 




Best, 

Amine 


De: "chebbi mohamed amine" <mohamed.amine.chebbi at univ-poitiers.fr> 
À: "Carson Holt" <carsonhh at gmail.com> 
Cc: maker-devel at yandell-lab.org 
Envoyé: Mercredi 12 Octobre 2016 11:44:21 
Objet: Re: [maker-devel] Combining and merging two Maker annotation gff files ? 



Thank you Carson for your quick response. Sorry, I have another question concerning Augustus Training. You posted previously in the mailing list a link to an explanation of Augustus training steps http://brie4.cshl.edu/pipermail/gmod-help/2012-June/001724.htm l . Unfortunately the link doesn't work anymore. Otherwise could you explain how to filter the gff file produced by the first run of Maker to get best full length ORF as a set of gene models to train Augustus ? 




De: "Carson Holt" <carsonhh at gmail.com> 
À: "Mohamed Amine CHEBBI" <mohamed.amine.chebbi at univ-poitiers.fr> 
Cc: maker-devel at yandell-lab.org 
Envoyé: Mardi 11 Octobre 2016 22:05:50 
Objet: Re: [maker-devel] Combining and merging two Maker annotation gff files ? 

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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