Non-syntenic ortholog is not present in pan-genome table

jtlovell / GENESPACE

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Non-syntenic ortholog is not present in pan-genome table #133

Closed xiaoyezao closed 5 months ago

xiaoyezao commented 11 months ago

Hi, I noticed that in the latest version, the non-syntenic ortholog (with tag *) is not present in pan-genome table even showNSOrtho = TRUE is used.

pangenome <- query_pangenes(gsParam, bed = NULL, refGenome = "sp21", transform = TRUE, showArrayMem = TRUE, showNSOrtho = TRUE, maxMem2Show = Inf, showUnPlacedPgs = TRUE )

Is this a planned update?

Thank you

jtlovell commented 10 months ago

Thanks for the note - I haven't noticed this ... did you complete a full orthofinder run (with orthologs). If so, what version are you running?