Gubbins output

[mariemh23]

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]

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]

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]

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

[mariemh23]

By micro recombination, I mean SNP (5 or 4 SNP) 2018-02-07 20:48 GMT+01:00 james hadfield <[email protected]>:

…

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 <#123 (comment)>, 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]

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]

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]

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]

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

[jameshadfield]

@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]

Thanks @jameshadfield. I use it well.

:)