This repository describes the code and analyses accompanying the MetaMap: An atlas of metatranscriptomic reads in human disease-related RNA-seq data manuscript.
The MetaMap bioinformatic pipeline screens human RNA-seq data for the presence of microbial and viral reads by re-inspecting the non-human-mapping read fraction. Simon et al. applied the pipeline to close to 150 terabytes of publicly available raw RNA-seq data from >17,000 samples from >400 studies relevant to human disease using state-of-the-art high performance computing systems from the Leibniz Supercomputing Centre in Garching, Germany.
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Detailed information about the MetaMap pipeline and how to execute it on your own data can be found at protocols.io.
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An R based tutorial describing the statistical analysis of the resulting output can be found in Tutorial_statistical_analysis.html/Rmd files.
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To facilitate interactive exploration of the MetaMap resource we have developed a webtool. By clicking on the following link you can access the webtool and agree with our data protection policy (as outlined here): MetaMap webtool. The code used to create the webtool can be found here.