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<div><span style="color: rgb(34, 34, 34); font-family: Arial, Helvetica, sans-serif; font-size: small; background-color: rgb(255, 255, 255);">Dear Maker developers,</span></div>
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Can Maker distinguish between simple and complex repeats from a gff3 file of pre-aligned repeats?</span><br style="color: rgb(34, 34, 34); font-family: Arial, Helvetica, sans-serif; font-size: small; background-color: rgb(255, 255, 255);">
<br style="color: rgb(34, 34, 34); font-family: Arial, Helvetica, sans-serif; font-size: small; background-color: rgb(255, 255, 255);">
<span style="color: rgb(34, 34, 34); font-family: Arial, Helvetica, sans-serif; font-size: small; background-color: rgb(255, 255, 255);">I'm trying to annotate a genome of a non-model Drosophila species and I've already generated a gff3 file with both simple
and complex repeats for this species. I would like to use this gff3 file as input for Repeat Masking so Maker won't have to align repeats from any library. My maker_opts.ctl file looks like this:</span><br style="color: rgb(34, 34, 34); font-family: Arial, Helvetica, sans-serif; font-size: small; background-color: rgb(255, 255, 255);">
<br style="color: rgb(34, 34, 34); font-family: Arial, Helvetica, sans-serif; font-size: small; background-color: rgb(255, 255, 255);">
<span style="color: rgb(34, 34, 34); font-family: Arial, Helvetica, sans-serif; font-size: small; background-color: rgb(255, 255, 255);">#-----Repeat Masking</span><br style="color: rgb(34, 34, 34); font-family: Arial, Helvetica, sans-serif; font-size: small; background-color: rgb(255, 255, 255);">
<span style="color: rgb(34, 34, 34); font-family: Arial, Helvetica, sans-serif; font-size: small; background-color: rgb(255, 255, 255);">model_org=</span><br style="color: rgb(34, 34, 34); font-family: Arial, Helvetica, sans-serif; font-size: small; background-color: rgb(255, 255, 255);">
<span style="color: rgb(34, 34, 34); font-family: Arial, Helvetica, sans-serif; font-size: small; background-color: rgb(255, 255, 255);">rmlib=</span><br style="color: rgb(34, 34, 34); font-family: Arial, Helvetica, sans-serif; font-size: small; background-color: rgb(255, 255, 255);">
<span style="color: rgb(34, 34, 34); font-family: Arial, Helvetica, sans-serif; font-size: small; background-color: rgb(255, 255, 255);">repeat_/path/to/te_proteins.fasta</span><br style="color: rgb(34, 34, 34); font-family: Arial, Helvetica, sans-serif; font-size: small; background-color: rgb(255, 255, 255);">
<span style="color: rgb(34, 34, 34); font-family: Arial, Helvetica, sans-serif; font-size: small; background-color: rgb(255, 255, 255);">rm_gff=/path/to/Dato_genome.Dato-</span><wbr style="color: rgb(34, 34, 34); font-family: Arial, Helvetica, sans-serif; font-size: small; background-color: rgb(255, 255, 255);"><span style="color: rgb(34, 34, 34); font-family: Arial, Helvetica, sans-serif; font-size: small; background-color: rgb(255, 255, 255);">first.full_mask.out.reformat.</span><wbr style="color: rgb(34, 34, 34); font-family: Arial, Helvetica, sans-serif; font-size: small; background-color: rgb(255, 255, 255);"><span style="color: rgb(34, 34, 34); font-family: Arial, Helvetica, sans-serif; font-size: small; background-color: rgb(255, 255, 255);">gff3</span><br style="color: rgb(34, 34, 34); font-family: Arial, Helvetica, sans-serif; font-size: small; background-color: rgb(255, 255, 255);">
<span style="color: rgb(34, 34, 34); font-family: Arial, Helvetica, sans-serif; font-size: small; background-color: rgb(255, 255, 255);">prok_rm=0</span><br style="color: rgb(34, 34, 34); font-family: Arial, Helvetica, sans-serif; font-size: small; background-color: rgb(255, 255, 255);">
<span style="color: rgb(34, 34, 34); font-family: Arial, Helvetica, sans-serif; font-size: small; background-color: rgb(255, 255, 255);">softmask=1</span><br style="color: rgb(34, 34, 34); font-family: Arial, Helvetica, sans-serif; font-size: small; background-color: rgb(255, 255, 255);">
<br style="color: rgb(34, 34, 34); font-family: Arial, Helvetica, sans-serif; font-size: small; background-color: rgb(255, 255, 255);">
<span style="color: rgb(34, 34, 34); font-family: Arial, Helvetica, sans-serif; font-size: small; background-color: rgb(255, 255, 255);">By using softmask=1 I understand that Maker will softmask only low complexity repeats (while complex ones will be hardmasked).
My question is whether Maker can distinguish between simple and complex repeats from the gff3 file in order to softmask only simple repeats. Also, do you think it would be better to only include complex repeats in the gff3 file and let Maker find simple repeats
on its own by using model_org=simple?</span><br style="color: rgb(34, 34, 34); font-family: Arial, Helvetica, sans-serif; font-size: small; background-color: rgb(255, 255, 255);">
<br style="color: rgb(34, 34, 34); font-family: Arial, Helvetica, sans-serif; font-size: small; background-color: rgb(255, 255, 255);">
<span style="color: rgb(34, 34, 34); font-family: Arial, Helvetica, sans-serif; font-size: small; background-color: rgb(255, 255, 255);">Thank you very much in advance.</span>
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<div><font color="#222222" face="Arial, Helvetica, sans-serif" size="2"><span style="background-color: rgb(255, 255, 255);">Best regards,</span></font></div>
<div><font color="#222222" face="Arial, Helvetica, sans-serif" size="2"><span style="background-color: rgb(255, 255, 255);">Santiago</span></font></div>
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