Dataset Open Access

Training Data for "Metatranscriptomics analysis using microbiome RNASeq data"

Bérénice Batut; Subina Mehta; Praveen Kumar; Pratik Jagtap; Saskia Hiltemann

Microbiomes play a critical role in host health, disease, and the environment.. Functional microbiome analysis which estimates the functional groups expressed by microbial community enables researchers to look beyond taxonomic composition and correlation with the condition under study. Using microbial community RNA-Seq data and subsequent metatranscriptomics workflows to elucidate the functional complement of the microbiome is gaining interest in the field.
This tutorial from Galaxy training network will introduce researchers to the basic concepts of metatranscriptomics data analysis. It takes in paired-end datasets of raw shotgun sequences (in FastQ format) as an input and:

  1. preprocess
  2. extract and analyze the community structure (taxonomic information)
  3. extract and analyze the community functions (functional information)
  4. combine taxonomic and functional information to offer insights into taxonomic contribution to a function or functions expressed by a particular taxonomy.

The dataset used in the tutorial comes from a time-serie analysis of a microbial community inside a bioreactor (Kunath et al, ISME, 2018). Only the data for one time point (1st) and a biological replicate (A) is analyzed here, after having been trimmed out the original file for the purpose of saving time and resources.

Files (175.8 MB)
Name Size
T1A_forward.fastqsanger
md5:0e8850e3e4bab1e53ba97d2669b11894
87.7 MB Download
T1A_HUMAnN_Gene_families_and_their_abundance.tabular
md5:e2f63d78ce678cb7b597a86247365bf7
348.1 kB Download
T1A_HUMAnN_Pathways_and_their_abundance.tabular
md5:f8cbfa6cf8911428d21f0f6ce53959bc
11.1 kB Download
T1A_MetaPhlAn_Predicted_taxon_relative_abundances.tabular
md5:9587fa3c931cd059bb87a48436702f7f
3.4 kB Download
T1A_reverse.fastqsanger
md5:15fe313682f196bd49c44bfb19f9ae9d
87.7 MB Download
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