All the most important taxonomic and functional analysis compositional abundance matrices created
during the pipeline run, can be found within the merged_tables/ folders within the corresponding
TAXprofiles or PWYprofiles/ folders.
These compositional tables include:
- Taxonomic compositional matrix for dataset - the taxonomic information and abundance from each
sample, collated into one non-redundant matrix. This is used for any taxonomic microbiome
analysis and statistical comparison between communities. Stored in
TAXprofiles/readsTAX_<DBname>/merged_tables/merged_Counts+TAX.txt
- Genetic compositional matrix for dataset - the gene information and abundance from each sample
collated into one non-redundant matrix. This is used for any gene-focused microbiome explorations.
Stored in PWYprofiles/<PWYdb_name>/merged_tables/merged_geneTPMtable.txt
- Pathway compositional matrix for dataset - the functional (inferred pathway) information and
abundance from each sample, collated into 1 non-redundant matrix. This is used for any functional
analyses of communities and statistical comparisons between them. Stored in
PWYprofiles/<DBname>PWYs.MP/merged_tables/merged_Counts+PWY.txt
All files in these folders have a generally similar structure. They represent an abundance matrix for
the dataset, inclusive of all the samples and various features (TAX or PWYs or GENEs). This
information however is presented in different ways:
1) the per-sample counts alone (merged_Counts.txt)
2) the features identities alone (merged_{TAX, PWY}.txt)
3) the per-sample counts with the features table adjoined, in various combinations: each rank/level as
separate columns (merged_Counts+{TAX, PWY}.txt), or concatenated together as lineage within 1
column (e.g. merged_Counts+Lineage.txt), or both (merged_Counts+TAX+Lineage.txt).
4) the per-sample abundance table (merged_Counts+Lineage.txt), presented as a json biom file
(merged_Counts+Llineage_json.biom).
These files present the same information but separated by format for convenient utilization in
downstream analytical tools.