Home - TealFurnholm/Strain-Level_Metatranscriptome_Analysis GitHub Wiki

Welcome to the Metatranscriptome wiki!

You can choose between doing direct read alignment to the Universal Gene Database.
OR
If you have metagenome data too, you can analyze it through my metagenome pipeline, and then align to the contigs.

This pipeline outputs

  1. The matched gene info with read counts and phylogeny/LCA
  2. The community phylogeny with quantitative data: gene counts and read counts (normalized), for use in Cytoscape (or excel if you just want a table)
  3. The functional analysis, including summary data: gene counts, read counts, alignment scores, top organism, and LCA of all organisms in community w/function. This analysis can then be put into a secondary functional analysis: https://github.com/TealFurnholm/-Omic_Functional_Analysis

If you have multiple conditions (eg. disease vs control), you can also do differential analysis too.

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