mitochodria isCircular equals to FALSE in EnsDb.Hsapiens.v86 and EnsDb.Mmusculus.v79

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foehn ▴ 100

@foehn-16281

Last seen 3.3 years ago

United States

Hi there,

I'm using R annotation packages EnsDb.Hsapiens.v86 and EnsDb.Mmusculus.v79. I notice that both of them annotate mitochondrial DNA to non-circular, which seems contrary to the biology

> as.data.frame(seqinfo(EnsDb.Hsapiens.v86))["M", ]
   seqlengths isCircular genome
MT      16569      FALSE GRCh38
> as.data.frame(seqinfo(EnsDb.Mmusculus.v79))["M", ]
   seqlengths isCircular genome
MT      16299      FALSE GRCm38

Does anyone know the reason it is so? Thanks.

R annotation ensembldb • 3.2k views

ADD COMMENT • link 6.2 years ago foehn ▴ 100

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Thanks for pointing this out. I'll have to check the perl routines that fetch the data from the Ensembl databases. Something might be wrong there. I posted an issue at the ensembldb repo (https://github.com/jotsetung/ensembldb/issues/86)

ADD REPLY • link 6.2 years ago Johannes Rainer ★ 2.1k

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In the perl function that I'm using to create the EnsDbs I'm using the Ensembl Perl API and in fact calling is_circular on each chromosome (slice). Seems that even for chromosome MT this returns 0 (i.e. FALSE). I did contact the Ensembl support to ask for details on that. I'll keep you updated.

ADD REPLY • link 6.1 years ago Johannes Rainer ★ 2.1k

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Thanks a lot @Johannes!

ADD REPLY • link 6.1 years ago foehn ▴ 100

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Got a reply from the Ensembl support: they are aware of this inconsistency but did not solve it so far. They are working on it, but it won't happen before the next release.