Question: AGP files in Ensembl
0
gravatar for rubic
4 weeks ago by
rubic180
United States
rubic180 wrote:

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?

ensembl agp assembly • 163 views
ADD COMMENTlink modified 4 weeks ago by Emily_Ensembl18k • written 4 weeks ago by rubic180

Tagging: Emily_Ensembl

ADD REPLYlink written 4 weeks ago by genomax67k

Tagging me doesn't do anything.

ADD REPLYlink written 4 weeks ago by Emily_Ensembl18k
1
gravatar for Emily_Ensembl
4 weeks ago by
Emily_Ensembl18k
EMBL-EBI
Emily_Ensembl18k wrote:

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

ADD COMMENTlink written 4 weeks ago by Emily_Ensembl18k

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

ADD REPLYlink written 4 weeks ago by rubic180
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