It’s my first time that I want to use galaxy specifically LEfse.
I have read the tutorial and it seems it’s easy to use but I think there is a problem which I don’t know what is it.
I exported my data from qiime2 and make it in a form of relative abundance and “biom with taxonomy.tsv” and then kept just genus level. if any row didn’t have genus level I used the higher taxa level but with () around the name.
but when I use LEfse the result doesn’t make sense. could you please let me know why?
I send you my data and the result picture.
From what you’ve sent, it looks like the program is running correctly, but that only one feature was differentially abundant with sufficiently different LDA. It looks like Carnobacterium are more abundant in the “beef” category compared to the “chicken” category. Since the sample size is small (4 per category), it’s not surprising to me that there aren’t many statistically significant differences between the groups.
I hope that helps!