No access to online leffse

Downstream analysis and statistics LEfSe
1

Hi,

I have no access to lefse through http://huttenhower.sph.harvard.edu/galaxy/
is there a problem in the server or is it not available any more.

Thanks so much for the help

2

I also have been unable to access yesterday and today.

3

Hello,
Thank you for letting us know about this, we’re working on a solution as we speak.
Best,
Meg

1 Like
4

Hello,
LEfSe should be working again, let me know if you have any continuing issues.
Best,
Meg

5

Great, thanks! That was quick :slight_smile:

could you please help me with a question related with the analysis?

I am following a post from a while ago but i can not find it was responded https://groups.google.com/g/lefse-users/c/SU2sxI0DIyc/m/xdjro3FSBgAJ
I have6 categories ( 5 treatments plus a treatment with water). I want all of the 5 treatments to be compared against the water treatment, the control.
Similar to what this post asked https://groups.google.com/g/lefse-users/c/SU2sxI0DIyc/m/xdjro3FSBgAJ , i thought that i could use the one-against-all option by putting as ¨reference¨ the water treatment, but there is no way to chose the reference group. is there anyway around?
For instance, would a all-against-all option be a possible option if i include a class with the 6 treatments and then a subclass with two categories , such as treated vs control? would that compare all the treatments against the control?

Hope i have been able to explain myself…

Many thanks in advance for all the help!

1 Like
6

Hi Iratxez,

Which software do you finally use to compare your five treatment groups with your water control group?

Best,

Bing

7

Hi,
Apologies for responding late to this. Unfortunately LEfSe doesn’t allow for the specification of a reference group. I’d recommend MaAsLin 2 to run this type of analysis.
Best,
Meg

8

Thank you for your reply.

I am using the LEfSe and MaAsLin2 at the same time, and find the common significant features identified by both LEfSe and MaAsLin2.

9

Hello,

I have been unable to access LEfSe through https://huttenhower.sph.harvard.edu/galaxy/ since last week. Could you please inform me if there is an alternative way to get access to it?Thank you.

1 Like
10

Hi @salma_M,

Thanks for reaching out! Apologies for this issue, please see my post here for additional information, No access to online LefSe - #5 by Kelsey_Thompson

Best,
Kelsey