MT2MQ is a tool to prepare metatrascriptomic results from ASaiM for further analysis with MetaQuantome, which currently only supports metaproteomic data. This tool has three modes:
Taxonomic: takes in genus-level MetaPhlAn2 results for each sample. The input files should be named as the sample.
- Output: a taxonomy file and an intensity file to use in Metaquantome's taxonomy mode. The "peptide" column name is "id" and the taxon column name is "tax".
Functional: takes in a single file of HUMAnN2 results, regrouped and renamed to GO terms, with all samples joined together into one table, and renormalized to CPM. See the MT2MQ functional workflow for these processing steps. User can choose which GO namespace(s) to include.
- Output: a function file and an intensity file to use in Metaquantome's functional mode. The "peptide" column name is "id" and the functional column name is "gos".
Functional/taxonomic: takes the same input as the functional mode. User can choose which GO namespace(s) to include.
- Output: a single tabular file including all GO terms and the taxa which express them and their abundances for each sample. This file cannot be used as input for Metaquantome.