issue with Clavel 2023
Closed this issue · 8 comments
Bug description
I noticed that three of the samples published in Clavel et al 2023 are missing from the metadata.
- MAJ38, PRJEB59233, ERS14555592,ERS14555591,ERS14555590,ERS14555589,ERS14555588,ERS14555587
- RAY1028, PRJEB59233, ERS14555627,ERS14555628
- RAY3030, PRJEB59233, ERS14555635,ERS14555636
Additional context
No response
Hi @theHatIsBack 🦅 👁️ !!!
You're right they aren't included, but this was because when looking at the results they did not have enough coverage to be considered a 'genome' (IMO).
Or do you disagree?
Its true that they are low coverage but I think there are two reasons for why they should be included:
- In Clavel et al 2023 MAJ75, MAJ46 & MAJ38 are combined together to produce a higher coverage genome as are RAY1015, RAY1028 & RAY3030.
- secondly for the sake of consistency, as there are other low coverage 'genomes' that are included like IMO2 from Guellil et al 2021 which if memory serves is approximately 0.3x
I see.
While I personally don't like the idea of mixing strains, j can see why people would do it.
Also fair enough with the Guellil, I guess I missed that one.
Fancy making a PR? 🌝
I just attempted to but it seems I can't create a branch?
when attempting to push the new branch created locally I got the following error
cameronrobertferguson@Camerons-MacBook-Pro AncientMetagenomeDir % git push --set-upstream origin clavel2023_update_info
ERROR: Permission to SPAAM-community/AncientMetagenomeDir.git denied to theHatIsBack.
fatal: Could not read from remote repository.
Please make sure you have the correct access rights
and the repository exists.
and I couldn't seem to add it through the github website either?
Ach! Will give you permissions in a bit - had to overhaul the permissions for the whole organisations recently...
You should have an invite for the organisation! Once accepted, please try again!
ok that should be the PR submitted now