The "seqtab.txt" file currently output by the TADA pipeline is not directly compatible with the Mia package, which we plan to transition to from Phyloseq.
According to Mia tutorial here:
"Abundance table (assay_taxa.csv): data matrix (features x samples); first column provides feature IDs, the first row provides sample IDs; other values should be numeric (abundances)."
Example:
|
C1 |
C2 |
C3 |
C4 |
C5 |
C6 |
C7 |
C8 |
C9 |
C10 |
| GAYR01026362.62.2014 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
| CVJT01000011.50.2173 |
1 |
0 |
1 |
1 |
0 |
0 |
0 |
5 |
1 |
4 |
| KF625183.1.1786 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
| AYSG01000002.292.2076 |
0 |
0 |
0 |
0 |
1 |
0 |
0 |
0 |
0 |
0 |
| CCPS01000022.154.1916 |
7 |
2 |
10 |
15 |
0 |
0 |
0 |
0 |
11 |
4 |
| KJ923794.1.1762 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
| CP006736.223921.225660 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
| GEMN01027092.33.1623 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
| EU622687.1.1587 |
0 |
23 |
14 |
43 |
9 |
5 |
2 |
21 |
8 |
7 |
| KY646024.1.1591 |
0 |
0 |
2 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
| JUOP01000215.81.1657 |
2 |
0 |
0 |
2 |
0 |
0 |
0 |
0 |
2 |
4 |
| JN628990.1.1569 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
| KF843412.1.1565 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
The "seqtab.txt" file currently output by the TADA pipeline is not directly compatible with the Mia package, which we plan to transition to from Phyloseq.
According to Mia tutorial here:
"Abundance table (assay_taxa.csv): data matrix (features x samples); first column provides feature IDs, the first row provides sample IDs; other values should be numeric (abundances)."
Example: