Questions About Scaffold Length And De Novo Annotation

Question

[Lhl]

Hi All,

Could anyone tell me more details about how assembled contig/scaffolds length influence de novo gene prediction? I know that short scaffolds length will for sure limit gene prediction. But i want know more details. Thanks a lot.

Cheers

Elzed

Answer 1

[Yannick Wurm]

If a gene is split between two scaffolds (ie. some exons on one; other exons on the other), the gene prediction software won't understand that they're the same gene --> and will thus give you 2 different gene models.

[Lhl]

Thanks. this makes sense to me.