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<div style="direction: ltr;font-family: Tahoma;color: #000000;font-size: 10pt;"><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>
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<div><span style="background-color: rgb(255, 255, 255);"><font color="#222222" face="Arial, Helvetica, sans-serif" size="2">Can Maker deal with a "dispersed_repeat" one-level features GFF3 file provided to the rm_gff option in the control file?</font></span>
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We're trying to annotate a genome of a non-model Drosophila species using a previously generated GFF3 file with repeats for this species. Some months ago, Carson Holt replied to a post (<a href="https://groups.google.com/g/maker-devel/c/BhBMTF8dze8/m/y-QwJYRFAQAJ">https://groups.google.com/g/maker-devel/c/BhBMTF8dze8/m/y-QwJYRFAQAJ</a>)
saying that "They (repeat models) must be match/match_part two level feature for rm_gff". However, all features on our GFF3 file are 'dispersed_repeat' one-level features.</div>
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Here is how our file looks like (extract of the file for a scaffold attached as well, repeats.gff3):</div>
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<div>##sequence-region scaffold1062|size32755 1 32755</div>
<div>scaffold1062|size32755 RepeatMasker dispersed_repeat 1 47 271 - . Target=DNAREP1_DM 26 73;ID=2740</div>
<div>scaffold1062|size32755 RepeatMasker dispersed_repeat 48 83 263 + . Target=Dbuz_kz3_5_36225 704 739;ID=2741</div>
<div>scaffold1062|size32755 RepeatMasker dispersed_repeat 340 386 299 - . Target=rnd-1_family-30 19 65;ID=2742</div>
<div>scaffold1062|size32755 RepeatMasker dispersed_repeat 349 387 247 + . Target=rnd-1_family-29 1 71;ID=2743</div>
<div>scaffold1062|size32755 RepeatMasker dispersed_repeat 388 430 240 + . Target=rnd-5_family-3333_TIR_P 3669 3713;ID=2744</div>
<div>scaffold1062|size32755 RepeatMasker dispersed_repeat 446 555 408 - . Target=rnd-1_family-15 16 138;ID=2745</div>
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I'm attaching both the log file and the CTL file for what it's worth (Dtest.log / maker_opts.ctl).</div>
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I wonder whether Maker handled right our rm_gff file, whether the generated output is reliable. If not, do you think modifying the GFF3 file manually duplicating each row and changing the third column to 'match/match_part' could do the trick?</div>
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Thank you very much in advance.</div>
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Best regards,</div>
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Santiago</div>
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