Hi all, 

I  am annotating my new plant genome now and am working with Maker and its very detailed tutorial (http://weatherby.genetics.utah.edu/MAKER/wiki/index.php/MAKER_Tutorial_for_WGS_Assembly_and_Annotation_Winter_School_2018) . I have read a few really helpful posts about Maker here as well, but i still have some questions. 

1. SNAP training. How do you actually know that it is enough to train and you can run your final Maker run? I have tried to run it several time and there is a difference in the number of genes every time. It is actually a kind of sinusoidal graph - number of genes are going up and down... So when do you stop? Or how do you know that SNAP is trained? Do you wait until the plateau? How many times did you do the training and why?

2. My genome has unusually high repeat content. This is why I decided to create its own repeat library with repeatModeler. The question is where on the option file do I add this repeat library? 

###THANKS a lot for your help, 
Alex
You can specify a custom repeat library (in FASTA format) with `rmlib` in the Repeat Masking section of the `make_opts.ctl` file

    #-----Repeat Masking (leave values blank to skip repeat masking)
    model_org=all #select a model organism for RepBase masking in RepeatMasker
    rmlib=repeatlibrary.fa #provide an organism specific repeat library in fasta format for RepeatMasker
    repeat_protein=/opt/maker/data/te_proteins.fasta #provide a fasta file of transposable element proteins
    rm_gff= #pre-identified repeat elements from an external GFF3 file
    prok_rm=0 #forces MAKER to repeatmask prokaryotes (no reason to change this), 1 = yes, 0 = no
    softmask=1 #use soft-masking rather than hard-masking in BLAST (i.e. seg and dust filtering)`

This is an example Repeat Masking section


You might also consider running ProtExcluder on the output of RepeatModeler

http://weatherby.genetics.utah.edu/MAKER/wiki/index.php/Repeat_Library_Construction-Basic

    # Run blastx then ProtExcluder to excluce known protein sequences from RepeatModeler library
    /usr/bin/blastx -num_threads 75 -db /genetics/elbers/maker/uniprot_sprot.fasta -evalue 1e-6 \
    -query repeatlibrary.fa -out repeatlibrary.fa.blast

    /opt/ProtExcluder1.1/ProtExcluder.pl -f 50 repeatlibrary.fa.blast repeatlibrary.fa
    # output of ProtExcluder is "temp"
    # rename temp to whatever you desire
    mv temp repeatlibrary.fa2
