Data upload error_.csv or .txt

MicrobiomeAnalyst
1

I am having difficulty understanding the correct format and structure required for data file submission in Microbiomeanalyst. The guidelines are not entirely clear to me, and I would appreciate more explicit instructions or examples to ensure data preparatino.

I am having difficulty understanding the correct format and structure required for data file submission in MetaboAnalyst. The guidelines are not entirely clear to me, and I would appreciate more explicit instructions or examples to ensure proper data preparation.

2

There are four types of input files:

  1. Feature (OTU/ASV) Abundance Table: Matrix containing sequence counts for each Amplicon Sequence Variant (ASV) or Operational Taxonomic Unit (OTU) across all samples.
  2. Taxonomic Annotation Table: Assignment table mapping each ASV/OTU to hierarchical taxonomic levels (domain to species) using a reference sequence database (e.g., SILVA, Greengenes, GTDB).
  3. Sample Metadata File: File containing sample identifiers, experimental variables, clinical covariates, and group classifications (e.g., disease status, treatment group, time point).
  4. Phylogenetic Tree (Optional): Evolutionary tree mapping relationships among ASV/OTU sequences, required for calculating phylogenetic diversity metrics (e.g., UniFrac, Faith’s PD).

Requirements #1 and #3 are similar to all other omics data, while #2 and #4 are more unique. In general, you don’t need to fully understand the data formats as they are standard formats generated by tools widely used by the community such as QIIME, DADA2, Mothur, etc.

MicrobiomeAnalyst accepts common data formats are described here. In addition, for each module in MicrobiomeAnalyst, there are example data sets at the data upload page. You can download them to view more details