search

jameshadfield / phandango

an interactive viewer for populations of bacterial genomes linked by a phylogeny
http://phandango.net
MIT License
113 stars 27 forks source link

Gubbins output #123

Open mariemh23 opened 6 years ago

mariemh23 commented 6 years ago

Hello,

I have an issue when i try to visualize the gubbins output. Could you help me, please? if I understood correctly, I have to add the gff file and the tree (from Gubbins) as well as the annotation file of the reference strain (which I used to launch gubbins). However, I get no block except in the line opposite the reference strain.

Thanks

jameshadfield commented 6 years ago

Hi @mariemh23 - that sounds like you've got the correct files. Could you have a look inside the gubbins GFF file and check that it did indeed find recombination blocks in sequences other than the reference?

mariemh23 commented 6 years ago

Yes , I checked my gff file and I got some micro recombination . Actually , i generated a graph with gubbins_drawer and I got others recombination but it does not specify the location of the recombination Maybe phandango only shows recombination blocks and not micro recombination

jameshadfield commented 6 years ago

I'm not familiar with "micro recombination" - @simonrharris what's going on here?

mariemh23 commented 6 years ago

By micro recombination, I mean SNP (5 or 4 SNP)

2018-02-07 20:48 GMT+01:00 james hadfield notifications@github.com:

I'm not familiar with "micro recombination" - @simonrharris https://github.com/simonrharris what's going on here?

— You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub https://github.com/jameshadfield/phandango/issues/123#issuecomment-363888619, or mute the thread https://github.com/notifications/unsubscribe-auth/AcnC1PepKjZMvV_vN-vRG3dPfVe0aLaMks5tSf4AgaJpZM4R4Uug .

-- Mariem Hanachi Phd student Laboratory of Bioinformatics, Mathematics and Statistics Institute Pasteur in Tunis +216 20 053 867

simonrharris commented 6 years ago

This may sound silly, but have you tried zooming in to where you think those small blocks should be? It may be that they are too small to see at full genome level in Phandango.

jameshadfield commented 6 years ago

If this is the case, we should make the blocks some min number of pixels. I think someone else mentioned this a while ago.

diaz13 commented 5 years ago

Hello @jameshadfield I used gubbins. After i wanted to use phandango to generate figures. But I do not see how to use phandango or how to install it ? Thank you

mariemh23 commented 5 years ago

No need to install. Just drag your files to the main page of the site https://jameshadfield.github.io/phandango/#/

jameshadfield commented 5 years ago

@diaz13 phandango doesn't need any installation, it's used by dropping your data files onto http://www.phandango.net (or https://jameshadfield.github.io/phandango, they're the same thing).

The wiki -- https://github.com/jameshadfield/phandango/wiki -- contains more details on file formats etc. If you have any further problems please open a new issue 👍

diaz13 commented 5 years ago

Thanks @jameshadfield. I use it well.

:)