issue with Clavel 2023 - Githubissues

SPAAM-community / AncientMetagenomeDir

Repository containing lists of all published ancient metagenomic (and related) samples and libraries

http://www.spaam-community.org/AncientMetagenomeDir/

Creative Commons Attribution 4.0 International

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issue with Clavel 2023 #1110

Closed theHatIsBack closed 9 months ago

theHatIsBack commented 12 months ago

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

jfy133 commented 11 months ago

Hi @theHatIsBack :eagle: :eye: !!!

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?

theHatIsBack commented 11 months ago

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

jfy133 commented 11 months ago

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? 🌝

theHatIsBack commented 11 months ago

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?

jfy133 commented 11 months ago

Ach! Will give you permissions in a bit - had to overhaul the permissions for the whole organisations recently...

jfy133 commented 11 months ago

You should have an invite for the organisation! Once accepted, please try again!

theHatIsBack commented 11 months ago

ok that should be the PR submitted now

alexhbnr commented 9 months ago

Fixed with PR #1111