Can't find any single copy orthologue sequences

[Dream-sugar]

Hi David, Thank you for developing this software. I would really appreciate your help if you could clarify my following doubts: When I use orthofinder to analyze 47 samples about 40 species of RNA-seq. The command I use is as follows: orthofinder -f pep/ . I always can't get any single copy gene sequences. When I reduce the sample of outgroups, there are 4 single copy gene. Is it species specificity? Or something else? Is this result normal? Looking forward to your help.

Best Wishes!

[davidemms]

Hi

That sounds very normal. If you increase the number of species and if you use RNA-seq data it becomes extremely unlikely that you will find many or any orthogroups which have one and only one gene present in every single species, it's just probability.

You can analyse the Orthogroups.GeneCount.tsv in Excel/python to identify orthogroups which meet more relaxed criteria. E.g. present in 95% of species and single-copy.

Best wishes David

[Dream-sugar]

Thank you very much for your answer, which is very useful to me. I hope you can write some relevant scripts to filter the corresponding sequences in your spare time