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USher: have been mutations displayed on the branch changed? or is it a bug ? #366
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It seems back to old version now. |
It works with branches but not with singlets |
could it a nextstrain issue? cc @corneliusroemer |
@FedeGueli as far as I can tell the behavior has not changed recently -- Nextstrain's Auspice viewer shows all mutations for a particular sample, but shows only the node's mutations for an internal node. Branch labels have the same behavior: they appear only for internal nodes, not for branches to single samples. Now that you mention it, it would be nice to have a way to see only the private mutations for a sample, but I don't know of a way to get that in Auspice. @corneliusroemer is this related to the feature request that you just made in nextstrain/auspice#1752 ? |
Thx @AngieHinrichs , maybe @aviczhl2 or @ryhisner would like to add their ideas this morning it didnt work as usual. Re singlets: i dont recall how it wss before. If it was already this way to.me this issue is solved. |
@AngieHinrichs i checked and it is not the same than before: |
I agree with Fede here. It's not possible to view the mutations on any given branch now, which makes it extremely hard to tell what mutations are unique to a given sequence. Right now I'm having to take screenshots of the mutations in a sequence at the base of a branch and the end of a branch and compare them to try to figure out what mutations are on that branch, which is extremely time-consuming and also likely to lead me top make mistakes. |
Wow, that sounds awful @ryhisner. I have not made any changes to usher.bio / hgPhyloPlace, so I guess this must be a change to Auspice. @corneliusroemer @jameshadfield is there any way in Auspice to see only the private mutations on a sample, instead of all mutations from root? |
Meanwhile @ryhisner there are alternatives to manually comparing all mutations, even if they're not ideal. nextstrain.org (Auspice) is displaying a JSON file (just text in a special format) generated by usher.bio. The file includes the private mutations for each sample. You can view that file by removing the "nextstrain.org/fetch/" part of a link like this:
-- not pretty, but I hope not as bad as manually comparing those lists. If you have a browser extension that pretty-prints JSON files, it may take a minute to digest it all, but then it should look something like this:
Easier on the eyes. Anyway, the private mutations are in there, we'll find some way to extract them for you. 🙂 |
Thank you, @AngieHinrichs! I hope this issue gets fixed, but in the meantime your tip will definitely save me time. |
Me and others noticed that today Usher (dev) not showing the private mutations of each branch while instead showing all the mutations of the sample at the end of the branch :
![Screenshot 2024-02-16 alle 10 06 09](https://private-user-images.githubusercontent.com/87669813/305360931-63d38f2d-2e10-4b8d-b188-fd80d7b92bd6.png?jwt=eyJhbGciOiJIUzI1NiIsInR5cCI6IkpXVCJ9.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.s1OSGp2QRBqnZPcg6NA1UQ7wsfUI8ythyWgawISTdqM)
![Screenshot 2024-02-16 alle 10 08 08](https://private-user-images.githubusercontent.com/87669813/305361464-30eb6eed-8d72-493a-9ff1-ad4c7cdcc4fc.png?jwt=eyJhbGciOiJIUzI1NiIsInR5cCI6IkpXVCJ9.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.V6HA_CCgHaNtwp3z_lGNA0oPna4lZUvoN7ybU3yoSmU)
https://nextstrain.org/fetch/genome-test.gi.ucsc.edu/trash/ct/subtreeAuspice1_genome_test_4d5a0_f1caa0.json?label=id:node_3753494
I dunno if it is a choice or something went wrong with some update.
In the case it is wanted, i suggest to revert to previous setting cause it was much more useful.
@AngieHinrichs
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