Fungal genome annotation

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Fungal genome annotation

Linnie Linnie
Dear maker team,

I am annotating a small fungal genome (~30Mb) and I have several questions as I move forward. My plan is to do:
1. customĀ repeat library
2. evidence-based maker (custom repeat library, repbase fungi database, te_proteins.fa, ESTs from a somewhat related organism, proteome from related organisms, transcripts from the same species)
3. train snap
4. maker run
5. re train snap (if it improves the models)
6. maker run
7. train Augustus
8. maker run
9. retrain augustus, if necessary
10. maker run
11. genemark
12. final maker run

My questions are:

a. Do I have to run RepeatMasker at every maker iteration?
b. Since I am dealing with a fungal genome, is it wise to change the maker_opts.ctl with singe_exon=1, keep_phreds=1, correct_es_fusion=1?Ā 
c. If so, should I keep those parameters in every maker iteration?

Thank you so much for your help!

Linnie

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