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davidemms / OrthoFinder

Phylogenetic orthology inference for comparative genomics
https://davidemms.github.io/
GNU General Public License v3.0
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How to get species-specific genes from OrthoFinder results..? #656

Closed pjyoti29 closed 2 years ago

pjyoti29 commented 2 years ago

Orthogroups_UnassignedGenes.tsv file contains all of the genes that were not assigned to any orthogroup. But then why they are given an orthogroup ID. Can we say these gene list specific to that particular species and can be used as species-specific genes.

thanks..!!

davidemms commented 2 years ago

Hi

These are genes that were not even clustered with any genes. As such, they are a subset of the species-specific genes. There are also species-specific genes which have multiple paralogs in that species, you can find them by looking in the file "Orthogroups/Orthogroups.GeneCount.tsv". If you create a 'Total' column (the sum for that row) then you can search for orthogroups where the number of genes in species X is equal to the Total.

Best wishes David