-
Notifications
You must be signed in to change notification settings - Fork 6
New issue
Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.
By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.
Already on GitHub? Sign in to your account
HOG taxonomy seems buggy #28
Comments
Hello! Thank you for reaching out! In the meantime, in this particular case you can obtain the same results as if you were using Hymenoptera as a clade of interest by using the taxid of Apocrita rather than the one of your species "-t 7400". Regarding the HOGs number, it is actually expected than the number of conserved HOGs is lower than the one of the lineage associated HOGs as the former is a subset of the later - only those HOGs found in more than 80% of the species of the clade. Best wishes, |
Hello I'm trying to understand how omark identyfies what taxonomic rank to use. I'm checking the OMArk result for an annotation of Bombus terrestris (common bee) and specifying the -r order flag it says that it is too narrow or it does not exist, however the one used in the default is Aculeata wich is the infraorder for this particular species, why is this happenning?.
Then the HOGs used to check the consistency are different to the ones used to check the completeness:
16727 HOGs are associated to the query's lineage and will be used for consistency assesment
6496 conserved ancestral HOGs will be used from completeness assesment
I'm including the options used and stderr, and stdout down below:
The text was updated successfully, but these errors were encountered: