Query Regarding Platypus genome

[Meenakshi Bagadia]

Hi,

I am working on Platypus genome. 

In UCSC, two versions are available .

1) Feb. 2007 (ASM227v2/ornAna2)

2)Mar. 2007 (WUGSC 5.0.1/ornAna1)

And in Ensembl , there is one version : OANA5, INSDC Assembly GCF_000002275.2, Dec 2005

Which version of UCSC is equivalent to Ensembl version.

And I need the Liftover files for hg19To ornAna2.

Thanks and regards

Meenakshi

 

[Jairo Navarro Gonzalez]

Hello Meenakshi,

Thank you for using the UCSC Genome Browser and your question regarding the platypus genome.

The ornAna1 and ornAna2 assemblies differ from the Ensembl assembly since these are old assemblies that were created before a RefSeq assembly was available for platypus. The ornAna1 assembly corresponds to Ensembl release, Ornithorhynchus_anatinus.OANA5, but they are not the same assembly. Comparing the ornAna2 and Ensembl assemblies, 201,246 of the contigs in each are identical. UCSC has 279 contigs that Ensembl does not, and Ensembl has 89,846 contigs that are not in the UCSC assembly. The UCSC platypus assemblies, ornAna1 and ornAna2, are almost identical. There are 201,522 contigs in common between ornAna1 and ornAna2, with one extra contig in ornAna1 not in ornAna2, and three additional contigs in ornAna2 not in ornAna1. Of the 200,154 sequences in the RefSeq assembly, 200,153 of them are found in ornAna2.

The genome assemblies are not the same, but they are almost identical.

Unfortunately, we do not have the alignment file going from hg19 to ornAna2, but there is an alternative. You can use liftOver to get the hg38 annotations on ornAna2 and then lift the resulting hg38 coordinates to hg19. You can find the necessary files on our download server:

hg38ToOrnAna2.over.chain.gz
hg38ToHg19.over.chain.gz

I hope this is helpful. If you have any further questions, please reply to gen...@soe.ucsc.edu.
All messages sent to that address are archived on a publicly-accessible Google Groups forum.
If your question includes sensitive data, you may send it instead to genom...@soe.ucsc.edu.

Jairo Navarro 
UCSC Genomics Institute

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