I am using mothur 1.39.5
I used make.lefse to generate a lefse table (from my subsample.shared, design and constaxonomy files) that I uploaded to Galaxy (tab-delimited) to go through lefse.
I really like that command because if you use LEFE (online on Galaxy with the output of make.lefse) you get associations at the OTU levels and also based on taxonomic assignation according to your favorite database/s (genus, family level, etc) which is great I think.
1-Is is possible to use the make.lefse output table to run mothur lefse command?
2- From Galaxy output (LDA effect size table) I get this for every OTU found associated to a specific class:
Bacteria,Firmicutes,Clostridia,Clostridiales,Lachnospiraceae,Lachnospiraceae_unclassified,Otu003, 4,600015036 Coccidia_Neg_Salino_Neg 4,234777037 0,000988941
Bacteria,Firmicutes,Clostridia,Clostridiales,Lachnospiraceae,Lachnospiraceae_unclassified,Otu003 4,600015036 Coccidia_Neg_Salino_Neg 4,234777037 0,000988941
so all OTUs are listed twice, sometimes with the exact LDA and p values but sometimes with slightly different values. Does anyone know why?
The make.lefse output seems normal (no double OTU numbers) apart from that there is a “|” character at the end of each otu while in galaxy example, the rows do no end by it.
When comparing this results (make.lefse + galaxy lefse) with the output of the lefse command in mothur, I get the same OTUs + some minor others when using make.lefse. So I guess the output (make.lefse + galaxy lefse) is ok at OTU level but could it affect the output for the other taxonomic levels such as:
Bacteria,Firmicutes,Clostridia,Clostridiales,Lachnospiraceae 5,807012495 Coccidia_Neg_Salino_Neg 5,141460065 0,000665218