How many genes get covered by my assembly

Question

[Ric]

Hello, I have a new assembly and I would like to know many genes get covered by the new assembly (completely or partially).

The gene annotation is in GFF3 format.

Is there any software available to do it or what would be the best way to do it?

Thank you in advance

[WouterDeCoster]

I've never used it, but as far as I know this is a job for BUSCO

[5heikki]

A good start would be to describe your problem in more detail

[h.mon]

The gene annotation is from another species? Another strain, same species? It is an annotation from your own assembly (then your question wouldn't make sense, but I have to ask anyway)?

[Ric]

Annotation is from another species.

[Farbod]

Dear Ric, Hi

You can also "Count your Full Length Transcripts".

Answer 1

[h.mon]

I will assume you have an unannotated assembly, and want to discover how many genes from an annotated close assembly are present in your assembly:

You can try RATT - it will transfer the annotation to the new assembly, and will output several stats about the outcome. You can also try QUAST, it has an option to compare a new assembly to a reference genome.

[Ric]

RATT requires embl file which I do not have and quast does not work with big genomes.

[h.mon]

RATT requires embl file

And apparently you did not search for convert gff to embl. Try EMBLmyGFF3, a software developed by someone with lots of experience on this issue.

From QUAST FAQ:

Current QUAST version is not optimised for large genomes yet.

It is not the same as "does not work". If you have the computational resources, it will work, if not, check FAQ #14.