Do we need to have separted embl files for each scaffold of the reference assembly to transfer the annotation to another assembly using RATT?

Question

[BioinfoNovice]

Hi,

I have an annotation of a reference genome that I would like to transfer to an updated version of the reference. Actually, some scaffolds have been splitted du to requirement of the NCBI. Therefore, the annotation needs to be changed in order to be compatible with the updated version.

I was told that RATT (Rapid Annotation Transfer Tool) could be used for my case. However, I have been trying and it's not working.

For the RATT pipeline, I need to have an embl file of the reference genome (generated using the reference sequence fasta file and an annotation gff file). I'm not quite sure whether I need to generate embl files for each scaffold or I can do for the whole genome at one file.

I would be glad to have some clarification.

Thank you very much in advance.

[Rox]

Hi,

I know this is a old post, by I have encountered the same problem as well with RATT.

Did you managed to find a solution ? when I download EMBL files for fruitfly and give it to RATT, is says that :

Sorry the embl file contained no sequence. Please specify a fasta file for the reference. Sorry the reference file wasn't generated corretly.

But the EMBL file did actually have a dna sequence at the end. And the fasta file reference the error refer to is an optional parameter. Any idea about this issue ? Thanks