Merge warning = 1

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Merge warning = 1

Jennifer Anderson
Hello,

I am working on the ab initiio annotation of a fungal genome, taking advantage of cDNA and protein evidence from other species. I am looking at my gff file following my first full attempt (hmm files from snap trained 2x, and GenemarkES).

I have not found information on what it means “merge_warning=1” at the end of the ID line, as in the example below.  Out of 6834 ID lines that include AED scores in this gff file, 5441 contain this warning. I would appreciate it if someone could point me in the right direction.


000030F|arrow maker gene 9255 9992 . - . ID=genemark-000030F|arrow-processed-gene-0.43;Name=genemark-000030F|arrow-processed-gene-0.43
000030F|arrow maker mRNA 9255 9992 . - . ID=genemark-000030F|arrow-processed-gene-0.43-mRNA-1;Parent=genemark-000030F|arrow-processed-gene-0.43;Name=genemark-000030F|arrow-processed-gene-0.43-mRNA-1;_AED=0.06;_eAED=0.06;_QI=0|0|0|1|1|1|2|0|220;_merge_warning=1
000030F|arrow maker exon 9838 9992 . - . ID=genemark-000030F|arrow-processed-gene-0.43-mRNA-1:2;Parent=genemark-000030F|arrow-processed-gene-0.43-mRNA-1
000030F|arrow maker exon 9255 9762 . - . ID=genemark-000030F|arrow-processed-gene-0.43-mRNA-1:1;Parent=genemark-000030F|arrow-processed-gene-0.43-mRNA-1
000030F|arrow maker CDS 9838 9992 . - 0 ID=genemark-000030F|arrow-processed-gene-0.43-mRNA-1:cds;Parent=genemark-000030F|arrow-processed-gene-0.43-mRNA-1
000030F|arrow maker CDS 9255 9762 . - 1 ID=genemark-000030F|arrow-processed-gene-0.43-mRNA-1:cds;Parent=genemark-000030F|arrow-processed-gene-0.43-mRNA-1

Best,

Jenni
















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Re: Merge warning = 1

Carson Holt-2
It’s an internal debugging related value used in the beta. It has no meaning for the general user and will eventually disappear.

—Carson


On Jun 12, 2018, at 9:59 AM, Jennifer Anderson <[hidden email]> wrote:

Hello,

I am working on the ab initiio annotation of a fungal genome, taking advantage of cDNA and protein evidence from other species. I am looking at my gff file following my first full attempt (hmm files from snap trained 2x, and GenemarkES).

I have not found information on what it means “merge_warning=1” at the end of the ID line, as in the example below.  Out of 6834 ID lines that include AED scores in this gff file, 5441 contain this warning. I would appreciate it if someone could point me in the right direction.


000030F|arrow maker gene 9255 9992 . - . ID=genemark-000030F|arrow-processed-gene-0.43;Name=genemark-000030F|arrow-processed-gene-0.43
000030F|arrow maker mRNA 9255 9992 . - . ID=genemark-000030F|arrow-processed-gene-0.43-mRNA-1;Parent=genemark-000030F|arrow-processed-gene-0.43;Name=genemark-000030F|arrow-processed-gene-0.43-mRNA-1;_AED=0.06;_eAED=0.06;_QI=0|0|0|1|1|1|2|0|220;_merge_warning=1
000030F|arrow maker exon 9838 9992 . - . ID=genemark-000030F|arrow-processed-gene-0.43-mRNA-1:2;Parent=genemark-000030F|arrow-processed-gene-0.43-mRNA-1
000030F|arrow maker exon 9255 9762 . - . ID=genemark-000030F|arrow-processed-gene-0.43-mRNA-1:1;Parent=genemark-000030F|arrow-processed-gene-0.43-mRNA-1
000030F|arrow maker CDS 9838 9992 . - 0 ID=genemark-000030F|arrow-processed-gene-0.43-mRNA-1:cds;Parent=genemark-000030F|arrow-processed-gene-0.43-mRNA-1
000030F|arrow maker CDS 9255 9762 . - 1 ID=genemark-000030F|arrow-processed-gene-0.43-mRNA-1:cds;Parent=genemark-000030F|arrow-processed-gene-0.43-mRNA-1

Best,

Jenni
















Page Title







När du har kontakt med oss på Uppsala universitet med e-post så innebär det att vi behandlar dina personuppgifter. För att läsa mer om hur vi gör det kan du läsa här: http://www.uu.se/om-uu/dataskydd-personuppgifter/

E-mailing Uppsala University means that we will process your personal data. For more information on how this is performed, please read here: http://www.uu.se/om-uu/dataskydd-personuppgifter/
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