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jorainer / ensembldb

This is the ensembldb development repository.
https://jorainer.github.io/ensembldb
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Not picking up circular DNA correctly #86

Open jorainer opened 5 years ago

jorainer commented 5 years ago

Check perl code and ensure circular DNA is correctly identified. See https://support.bioconductor.org/p/114611/ for the original question.

jorainer commented 5 years ago

Reply from Ensembl support:

Dear Rainer,

On 30/10/2018 11:07, Rainer Johannes wrote: I was puzzled that is_circular on the mitochondrial DNA returns 0. Below is the code I used - eventually there is something wrong with it. I'm using the Perl API version 94 and perl 5, version 18, subversion 0 (v5.18.0).

You are correct, and we're aware of the inconsistency.

So far, we've never put any effort into correcting it in order to better reflect biological reality but we're gonna solve the issue.

Unfortunately, it won't happen straight away as we have to investigate the impact of the change across several species DBs. Likely to happen for the next release.

Hope that helps,

Alessandro

jorainer commented 5 years ago

We need to check with the next Ensembl release whether it is fixed.

jorainer commented 2 years ago

Still not fixed (see issue #133).