MT2MQ one Metatranscriptomics data

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I am running a Metatranscriptomics pipeline on several samples from mice caeca and I would like to combine the results for each sample using the MT2MQ function in functional mode. However I fail to understand the format of the input file. Could someone detail the format of the input file and the steps to make it from each individual sample file ?

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Welcome, @Adrnfr

This is just a quote from the tool form, and hopefully you found this already! Both of those upstream tools are in Galaxy, and each is also included in tutorials – scroll to the very bottom of the tool form to find those. Running tutorial data through those upstream tools would provide an exact file to compare to.

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MT2MQ: Metatranscriptomics to Metaquantome

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.