[maker-devel] Repeats...

[Panos Ioannidis]

Hi guys,

I have finished running Maker on my genome, but get >800 genes (out of
~20,000) that have similarity to transposases. Except from RepBase, have
also built a species-specific repeat library, so it's weird that I still
have quite a few transposases in my gene set...

The repeat masking-related parameters in my maker-opts.ctl file are:

model_org=all #select a model organism for RepBase masking in RepeatMasker
rmlib=consensi.fa.classified #provide an organism specific repeat library
in fasta format for RepeatMasker
repeat_protein=/Home/pioannid/Programs/maker/data/te_proteins.fasta
#provide a fasta file of transposable element proteins for RepeatRunner
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)

Does anyone have an idea why I'm getting so many transposases?

Thanks,
Panos
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