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bpt26 / usher_wiki

docs holder for usher wiki
GNU General Public License v3.0
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Nodes_ids do not correspond between tree.nh and mutation.tsv #6

Open akograf opened 2 years ago

akograf commented 2 years ago

Hi, Thanks and congratulations for such great tool! I'm using matUtils --translate to generate a tsv file with the mutations in my tree nodes. However when comparing node_ids in this tsv file and in my tree.nh, they do not correspond. This is not happening with all nodes, it is more frequent in deeper nodes.

Thanks

akograf commented 2 years ago

Updating my issue: it was apparently solved when I generated a new newick tree using matUtils extract -i tree.pb -t tree.nh . Previously my tree was generated during the process of adding new sequences to a tree with usher command. Wherever, my new issue is that the mutation table generated with the new tree does not contemplate all nodes of the tree. Any thoughts?

AngieHinrichs commented 2 years ago

Hi @akograf - this repository is for documentation of UShER, not the actual usher and matUtils programs -- those are in yatisht/usher. It looks like the only watchers of this documentation repository are @bpt26 (who has moved on from the project) and I, not @yatisht and @jmcbroome who are the primary developers of usher and matUtils.

(@yatisht and @jmcbroome, you probably should watch this repo 🙂)

akograf commented 2 years ago

Ops, sorry. I will repost my issues in the right place. Thanks!

Em sex., 14 de jan. de 2022 às 15:55, Angie Hinrichs < @.***> escreveu:

Hi @akograf https://github.com/akograf - this repository is for documentation of UShER, not the actual usher and matUtils programs -- those are in yatisht/usher https://github.com/yatisht/usher. It looks like the only watchers of this documentation repository are @bpt26 https://github.com/bpt26 (who has moved on from the project) and I, not @yatisht https://github.com/yatisht and @jmcbroome https://github.com/jmcbroome who are the primary developers of usher and matUtils.

@.*** https://github.com/yatisht and @jmcbroome https://github.com/jmcbroome, you probably should watch this repo 🙂)

— Reply to this email directly, view it on GitHub https://github.com/bpt26/usher_wiki/issues/6#issuecomment-1013375456, or unsubscribe https://github.com/notifications/unsubscribe-auth/ACUSEC6NTJQWOFNC4X3KRK3UWBWQLANCNFSM5LZGISDQ . Triage notifications on the go with GitHub Mobile for iOS https://apps.apple.com/app/apple-store/id1477376905?ct=notification-email&mt=8&pt=524675 or Android https://play.google.com/store/apps/details?id=com.github.android&referrer=utm_campaign%3Dnotification-email%26utm_medium%3Demail%26utm_source%3Dgithub.

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yatisht commented 2 years ago

Thanks for the suggestion, @AngieHinrichs. I am watching this repo now.