The generated file seems to be different from the example？

[ZhangPY-bioinformatics]

SNAP does a great job but I've had some issues using it lately..
I found that the generated ZFF file does not contain Einit and Eterm, which means that the predicted genes only have exon entries and it is impossible to know which exons belong to the same gene.
When I checked gff3_to_zff.pl, I was surprised to find that this pl file does not output the information of Einit and Eterm, because the code does not seem to be able to achieve this function.
So how can I use it so that I can know the gene-level distribution of the predicted results instead of just the exon? This is very important for evaluating indicators such as BUSCO. Thanks for your help.

[iankorf]

SNAP definitely does make Einit and Eterm exons. If your sequences are small, maybe you won't see them, but for longer sequences, you definitely will. For training purposes, fathom calculates its own Einit and Eterm because historically, many people omitted that information.

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On Aug 17, 2024, at 4:12 AM, ZhangPY-bioinformatics ***@***.***> wrote: SNAP does a great job but I've had some issues using it lately.. I found that the generated ZFF file does not contain Einit and Eterm, which means that the predicted genes only have exon entries and it is impossible to know which exons belong to the same gene. When I checked gff3_to_zff.pl, I was surprised to find that this pl file does not output the information of Einit and Eterm, because the code does not seem to be able to achieve this function. So how can I use it so that I can know the gene-level distribution of the predicted results instead of just the exon? This is very important for evaluating indicators such as BUSCO. Thanks for your help. — Reply to this email directly, view it on GitHub, or unsubscribe. You are receiving this because you are subscribed to this thread.Message ID: ***@***.***>