low mapping

[paul-bio]

Ask away!

Hi, I just mapped my pore-c data to the reference genome and got a very low mapping rate.

And here is the parameter I used.

[sarahjeeeze]

Hi, you don't need to use porechopped reads and how are you producing the reference you are using, just thinking if its an assembly and there is lots of contigs in their it might not work well. We usually use the GCA reference. If you could share more details about your input files it may help

[paul-bio]

Hi @sarahjeeeze,

I’ve assembled a draft genome using PacBio Revio, resulting in 40 scaffolds with a BUSCO score of C:98.9% [S:97.8%, D:1.1%], F:0.4%, M:0.7%, n:3640. I believe this indicates a well-assembled draft genome, but I would like to scaffold it to the chromosome level.

Since there is no reference genome available for this species, I was considering using my draft genome as the reference.

Also, does this program require porechopped (trimmed reads) for mapping to the reference genome?

Thank you for your support!