[ensembl-dev] Gorilla assembly coverage depth

[William Spooner]

Thanks for the heads-up Greg,

This meta_key is certainly used by the Compara ProteinTrees pipeline (Bio::EnsEMBL::Compara::RunnableDB::ProteinTrees::GroupGenomesUnderTaxa), although I don't know what the downstream ramifications of the 'low' (basically not 'high' or '6X') setting are. I tend to set everything to 'high' to be on the safe side.

Will

On 15 Sep 2011, at 18:36, Gregory Jordan wrote:

> I understand that things in the 'meta' table tend to be for internal use only. But the assembly coverage depth information is only accessible from there, and surely this can't be accurate anymore:
> 
> > mysql -uensro -hens-livemirror -e "select * from gorilla_gorilla_core_64_31.meta where meta_key='assembly.coverage_depth'\G"
> *************************** 1. row ***************************
>    meta_id: 81
> species_id: 1
>   meta_key: assembly.coverage_depth
> meta_value: low
> 
> I doubt many people are actually using this undocumented information... but it caught me off guard, and it would be a shame for someone attempting to filter out low-coverage genomes to end up throwing the baby out with the bathwater, so to speak!
> 
> Cheers,
>  greg
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--
William Spooner
whs at eaglegenomics.com
http://www.eaglegenomics.com