Comments (14)
@sjackman it sure doesn't! I'd never seen results like that, but I only work with small viruses. How should this be marked up in the GFF3?
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Also, I don't suppose you could link me to a fasta sequence which would produce the data with introns, so I can test?
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Dang, you're fast. I'll get you some data.
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Here you go. Thanks! https://gist.github.com/sjackman/31cd4e17347ff1af488c
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@sjackman (never had comments on gists, I'm assuming it emails you, but in case it doesn't...)
would you mind sharing the command you ran this with? As of Aragorn v1.2.36 I didn't seem to be able to produce any headers with a )i( sequence in them, despite trying a number of configurations.
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No, I didn't get a notification from the gist. That seems like a GitHub issue/bug.
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Sorry, I meant to post the shell command and forgot.
aragorn -gcbact -i -c -w -o aragorn.tsv sample.fa
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brilliant, cheers. I'll ping you when I have a fix in place
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I'll mention that I've only ever seen a single intron. I have no idea whether ARAGORN could possibly output multiple introns. Thanks, Eric!
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Good to know. Having never worked with anything other than bacteriophages, I appreciate the insight.
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@sjackman not sure how familiar you are with the aragorn/maker/etc, but in the gff3 file you posted I'm having a bit of trouble rationalising a couple of the feature locations:
1 tRNA-Lys c[1533,4118] 34 (ttt)i(39,2512)
7 tRNA-Met c[26588,26660] 34 (cat)
8 tRNA-Tyr [26850,27468] 559 (ata)i(36,523)
becomes:
1 maker tRNA 1534 4115 100 - . ID=tRNA1;Parent=gene1;Name=trnK-UUU;_AED=0.48;_eAED=0.48;_QI=12|1|1|1|0|0|2|1|19
1 maker tRNA 26588 26660 100 - . ID=tRNA7;Parent=gene7;Name=trnM-CAU;_AED=0.00;_eAED=0.00;_QI=0|-1|1|1|-1|0|1|1|24
1 maker tRNA 26850 27468 100 + . ID=tRNA8;Parent=gene8;Name=trnV-UAC;_AED=0.48;_eAED=0.48;_QI=0|1|1|1|0|0|2|1|25
In the tRNA1
, the location is modified, +1 on the left hand, and -3 on the right, whilst in tRNA2
, the location is untouched. Given that the tRNA runs the full length of the feature, and that the other intron containing tRNA has an umodified location, I can't attribute it to the presence/absence of an intron. Is this a maker bug? Are you familiar enough to say?
I was just checking my work against the "reference", when I noticed a couple of these sorts of discrepancies.
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Hi, Eric. Very sorry. I should have mentioned that the GFF is generated not de novo but by aligning tRNA sequences from a difference (very closely related) species to the reference by MAKER using Exonerate. So, the coordinates of the de novo ARAGORN features and the MAKER/Exonerate features may not agree exactly.
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@sjackman no worries, not a problem. That explains the differences!
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Seems that I missed a lot! Thanks @erasche for fixing this.
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