[maker-devel] Maker annotation file not recognized by gff3toGenePred of UCSC Genome Browser
Carson Holt
carsonhh at gmail.com
Tue Aug 25 10:51:59 MDT 2015
You have edited the file in a way that broke it. Gene maker-scaffold10370-exonerate_est2genome-gene-0.0 previously had two separate transcript sequences (mRNA-1 and mRNA-2). You have deleted mRNA-1, but some of it’s children exons still exist. Notice that some exons have two parents, and you have deleted one of the parents without removing the parent relationship.
—Carson
> On Aug 20, 2015, at 9:37 AM, Xin Huang <xh33 at georgetown.edu> wrote:
>
> Dear Developer,
>
> I was trying to use a mixed GFF3 file to do some analysis, which includes genome-level gene predictions and manually curated annotations. I replaced the gene prediction by Maker annotations where appropriate. And a sample of the blended GFF3 file is as follows:
>
> scaffold10370 GLEAN mRNA 3918 18376 0.920154 + . ID=CCG000529.1;source_id=Aalb_GLEAN_10002648;
> scaffold10370 GLEAN CDS 3918 3983 . + 0 Parent=CCG000529.1;
> scaffold10370 GLEAN CDS 4521 4598 . + 0 Parent=CCG000529.1;
> scaffold10370 GLEAN CDS 17407 17516 . + 0 Parent=CCG000529.1;
> scaffold10370 GLEAN CDS 17588 17767 . + 1 Parent=CCG000529.1;
> scaffold10370 GLEAN CDS 18238 18376 . + 1 Parent=CCG000529.1;
> scaffold10370 maker gene 32452 54508 . - . ID=maker-scaffold10370-exonerate_est2genome-gene-0.0;Name=AAEL004146
> scaffold10370 maker mRNA 32452 54508 44204 - . ID=maker-scaffold10370-exonerate_est2genome-gene-0.0-mRNA-2;Parent=maker-scaffold10370-exonerate_est2genome-gene-0.0;Name=maker-scaffold10370-exonerate_est2genome-gene-0.0-mRNA-2;aED=0.00;eAED=0.00;qI=376|1|1|1|0|0|5|316|548
> scaffold10370 maker exon 32452 33011 . - . ID=maker-scaffold10370-exonerate_est2genome-gene-0.0-mRNA-2:exon:15;Parent=maker-scaffold10370-exonerate_est2genome-gene-0.0-mRNA-2
> scaffold10370 maker exon 35140 35388 . - . ID=maker-scaffold10370-exonerate_est2genome-gene-0.0-mRNA-1:exon:12;Parent=maker-scaffold10370-exonerate_est2genome-gene-0.0-mRNA-1,maker-scaffold10370-exonerate_est2genome-gene-0.0-mRNA-2
> scaffold10370 maker exon 35455 36119 . - . ID=maker-scaffold10370-exonerate_est2genome-gene-0.0-mRNA-1:exon:11;Parent=maker-scaffold10370-exonerate_est2genome-gene-0.0-mRNA-1,maker-scaffold10370-exonerate_est2genome-gene-0.0-mRNA-2
> scaffold10370 maker exon 36443 36777 . - . ID=maker-scaffold10370-exonerate_est2genome-gene-0.0-mRNA-1:exon:10;Parent=maker-scaffold10370-exonerate_est2genome-gene-0.0-mRNA-1,maker-scaffold10370-exonerate_est2genome-gene-0.0-mRNA-2
> scaffold10370 maker exon 53979 54508 . - . ID=maker-scaffold10370-exonerate_est2genome-gene-0.0-mRNA-1:exon:9;Parent=maker-scaffold10370-exonerate_est2genome-gene-0.0-mRNA-1,maker-scaffold10370-exonerate_est2genome-gene-0.0-mRNA-2
> scaffold10370 maker five_prime_UTR 54133 54508 . - . ID=maker-scaffold10370-exonerate_est2genome-gene-0.0-mRNA-2:five_prime_utr;Parent=maker-scaffold10370-exonerate_est2genome-gene-0.0-mRNA-2
> scaffold10370 maker CDS 53979 54132 . - 0 ID=maker-scaffold10370-exonerate_est2genome-gene-0.0-mRNA-2:cds;Parent=maker-scaffold10370-exonerate_est2genome-gene-0.0-mRNA-2
> scaffold10370 maker CDS 36443 36777 . - 2 ID=maker-scaffold10370-exonerate_est2genome-gene-0.0-mRNA-2:cds;Parent=maker-scaffold10370-exonerate_est2genome-gene-0.0-mRNA-2
> scaffold10370 maker CDS 35455 36119 . - 0 ID=maker-scaffold10370-exonerate_est2genome-gene-0.0-mRNA-2:cds;Parent=maker-scaffold10370-exonerate_est2genome-gene-0.0-mRNA-2
> scaffold10370 maker CDS 35140 35388 . - 1 ID=maker-scaffold10370-exonerate_est2genome-gene-0.0-mRNA-2:cds;Parent=maker-scaffold10370-exonerate_est2genome-gene-0.0-mRNA-2
> scaffold10370 maker CDS 32768 33011 . - 1 ID=maker-scaffold10370-exonerate_est2genome-gene-0.0-mRNA-2:cds;Parent=maker-scaffold10370-exonerate_est2genome-gene-0.0-mRNA-2
> scaffold10370 maker three_prime_UTR 32452 32767 . - . ID=maker-scaffold10370-exonerate_est2genome-gene-0.0-mRNA-2:three_prime_utr;Parent=maker-scaffold10370-exonerate_est2genome-gene-0.0-mRNA-2
>
> This file does not pass the GFF3 online validator from GenomeTools with the following error message:
>
> GenomeTools error: Parent "maker-scaffold10370-exonerate_est2genome-gene-0.0-mRNA-1" on line 1456 in file "/var/www/servers/genometools.org/htdocs/cgi-bin/gff3/Aalbo.gff <http://genometools.org/htdocs/cgi-bin/gff3/Aalbo.gff>" was not defined (via "ID=")
>
> And when I tried to use gff3toGenePred to convert GFF3 to the refflat format, I got the following parsing errors (samples):
>
> Can't find annotation record "maker-scaffold10370-exonerate_est2genome-gene-0.0-mRNA-1" referenced by "maker-scaffold10370-exonerate_est2genome-gene-0.0-mRNA-1:exon:12" Parent attribute
>
> Can't find annotation record "maker-scaffold10370-exonerate_est2genome-gene-0.0-mRNA-1" referenced by "maker-scaffold10370-exonerate_est2genome-gene-0.0-mRNA-1:exon:11" Parent attribute
>
> Can't find annotation record "maker-scaffold10370-exonerate_est2genome-gene-0.0-mRNA-1" referenced by "maker-scaffold10370-exonerate_est2genome-gene-0.0-mRNA-1:exon:10" Parent attribute
>
> Can't find annotation record "maker-scaffold10370-exonerate_est2genome-gene-0.0-mRNA-1" referenced by "maker-scaffold10370-exonerate_est2genome-gene-0.0-mRNA-1:exon:9" Parent attribute
>
> Can't find annotation record "maker-scaffold1193-exonerate_est2genome-gene-2.0-mRNA-2" referenced by "maker-scaffold1193-exonerate_est2genome-gene-2.0-mRNA-1:exon:114" Parent attribute
>
> Can't find annotation record "maker-scaffold16459-exonerate_est2genome-gene-0.0-mRNA-1" referenced by "maker-scaffold16459-exonerate_est2genome-gene-0.0-mRNA-1:exon:118" Parent attribute
>
> Can't find annotation record "maker-scaffold16459-exonerate_est2genome-gene-0.0-mRNA-1" referenced by "maker-scaffold16459-exonerate_est2genome-gene-0.0-mRNA-1:exon:119" Parent attribute
>
> Can't find annotation record "maker-scaffold16459-exonerate_est2genome-gene-0.0-mRNA-1" referenced by "maker-scaffold16459-exonerate_est2genome-gene-0.0-mRNA-1:exon:120" Parent attribute
>
> Can't find annotation record "maker-scaffold16459-exonerate_est2genome-gene-0.0-mRNA-1" referenced by "maker-scaffold16459-exonerate_est2genome-gene-0.0-mRNA-1:exon:121" Parent attribute
>
> What could have been the issue in the annotation file or the way I used the file? Any feedback will be highly appreciated!
>
> Sincerely,
>
> Xin Huang
> _______________________________________________
> maker-devel mailing list
> maker-devel at box290.bluehost.com
> http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://yandell-lab.org/pipermail/maker-devel_yandell-lab.org/attachments/20150825/1658dfd1/attachment-0003.html>
More information about the maker-devel
mailing list