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maggimars / Tara-Phaeo

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annotate orthogroups #6

Open maggimars opened 3 years ago

maggimars commented 3 years ago

Next step, I think, is to try to annotate the orthogroups from the Phaeo transcriptome/genomes ...

Originally posted by @maggimars in https://github.com/maggimars/Tara-Phaeo/issues/4#issuecomment-755062840

halexand commented 3 years ago

KEGG, pfam, KOG?

maggimars commented 3 years ago

Those were the ones I was thinking about. Any additional?

maggimars commented 3 years ago

make plots for % annotated out of core genes and noncore genes

maggimars commented 3 years ago

kegg_annotation_plot This plot shows the breakdown of orthogroup assignments for the genes in each transcriptome/genome that were annotated with KEGG ko values.

orthogroups_annotated This plot shows the proportion of genes within each orthogroup category that could be annotated with KEGG. The numbers on the bars show are total number of genes in that category.

Overall I am not seeing any particularly interesting patterns, but KEGG has low annotation rates for phaeo and I think protists in general. I am currently working on the same plots for pfam (just waiting on the annotations for a few strains to finish).