AGP files in Ensembl

Question

[rubic]

Hi,

Does anyone know where can AGP files be downloaded from Ensembl's website?

I'm using Ensembl's annotations for several genomes but can only find AGP files for them on NCBI and unfortunately for several of the genomes Ensembl's scaffold names do not match those of NCBI's.

For example the marmoset GTF in Ensembl (Callithrix_jacchus.ASM275486v1.95.gtf) lists these scaffold names: NTIC01000001.1, NTIC01000002.1, NTIC01001061.1, .. Whereas in the latest marmoset assembly at NCBI (https://www.ncbi.nlm.nih.gov/genome/?term=marmoset) the genome is in chromosomes and their RefSeq names are: NC_013896.1, NC_013897.1, NC_013898.1, ..

Which is what appears in the AGP file at NCBI.

So either Ensembl has its own AGP files using the scaffold names it is using or a table mapping between its scaffold names and those of RefSeq.

Any idea?

[GenoMax]

Tagging: Emily_Ensembl

[Emily]

Tagging me doesn't do anything.

Answer 1

[Emily]

The mapping between the chromosome and scaffold names can be found in the seq_region_synonym table in the Ensembl MySQL database.

[rubic]

Thanks a lot @Emily_Ensembl. Can that table somehow be retrieved using Bioconductor's biomaRt? Or is only retrievable using MySQL?