[maker-devel] Possible error in tRNA annotation by maker

[Carson Holt]

Do you have a small test contig I could use to duplicate the error?  That
will make it easier to fix.

Thanks,
Carson

From:  Jacques Dainat <jacques.dainat at imbim.uu.se>
Date:  Friday, May 23, 2014 at 1:56 AM
To:  <maker-devel at yandell-lab.org>
Subject:  [maker-devel] Possible error in tRNA annotation by maker

Hi,
I would like to submit a possible error that occurs by using the tRNA
annotation by maker.
I saw the problem in the gff result file. The problem occurs in only and for
all the tRNA who have an intron and that are in the + strand. Indeed, in
this case the strand of one of the exon seems to be wrong (see the example
below).

As exemple we have:
scaffold6501 maker gene 2126 2230 . + . XXX
scaffold6501 maker tRNA 2126 2230 . + . XXX
scaffold6501 maker exon 2185 2230 . - . XXX
scaffold6501 maker exon 2126 2163 . + . XXX

Theoretically, we should obtain:
scaffold6501 maker gene 2126 2230 . + . XXX
scaffold6501 maker tRNA 2126 2230 . + . XXX
scaffold6501 maker exon 2126 2163 . + . XXX
scaffold6501 maker exon 2185 2230 . + . XXX

kind regards,

Jacques Dainat, PhD
BILS (Bioinformatics Infrastructure for Life Sciences)

Adress: (room E10:3312)
Uppsala University, BMC
Department of Medical Biochemistry Microbiology, Genomics
Husargatan 3, box 582
S-75123 Uppsala Sweden

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