I am newby to Qiime2, but with firum supprt I have solved a series of probem.
Thank in advance.
But I have a trouble with the LEfSE analysis. Briefly, I have follwed the indication of the Dr Bemjamin obtaining the file in txt. I have tried to modified this file adding two raws in order to include Class- Subclass but when I switch to Galaxy there is this problem:
File “/shed_tools/testtoolshed.g2.bx.psu.edu/repos/george-weingart/lefse/a6284ef17bf3/lefse/format_input.py”, line 433, in feats = add_missing_levels(feats) File "/shed_tools/testtoolshed.g2.bx.psu.edu/
I thought that y file was correctly formatted but I do not understand the problem or how to provide a correct txt.
To complete the file I follwed the instruction found on this forum: by using excel (to add the lacking information) and then saving in txt. I also controlled, example file on galaxy.
I do not understand the trouble. Is possibile that step in excel has modified the file?
The error that you cannot see that I can only see when I run LEFSE on my local machine is this: "ValueError: could not convert string to float: "5,31E+13" In my US-centric view of the world, the LEFSE program doesn't seem to recognize commas as decimal points.
Thank you so much for your help.
I was not able to sostitute all “,” in “.” in excel before creating the file.txt.
What LEFSE “software” do you use? , Becouse I tried on R with phyloseq object but I did not obtain any result. Additionaly, follwoing diverse tutorail on LEFSE-R-Phyloseq I am not able to have LEFSE analysis. in other words I had to use LEFSE con galaxy for this reasons.
I have tried with the txt file that you have provided in Galaxy.
If I discard the sub-class raw, for example, I can do the analysis, but without any result.
It is clear that one of the problem is the “,” in the file, but then I do not understand what is the mistake: class/ subclass?, define raw o column on galaxy?
I will try again strating from qiime2…(unfortunatly, some guides have been made for qiime1)
Yeah, I’ve had this debate in the past regarding classes/subclasses, if you read Segata’s publication it’s hard to interpret exactly what they mean by classes and subclasses - I think I can’t answer that for you as it would depend on your analysis. I can tell you that using the Mercurial/Github code from way back when that file runs. I get Porphorymonas with your classes/subclasses. I can go and delve into the code for you. Ben
I tried your suggestion to use mercurial/GitHub code. I would like to use phyloseq object, but it appears quit impossible in R 3.6.
LEfSe in Galaxy is not clear (data.txt or other parameters) or almost sets up for qiime1.
I would standardize my analysis from qiime2 (first stesps) to R (second steps and plotting).
Thank you in advance for your help