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qbic-pipelines / rnadeseq

Differential gene expression analysis and pathway analysis of RNAseq data
MIT License
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Pathway analysis for metatranscriptomics #47

Closed d4straub closed 4 years ago

d4straub commented 5 years ago

The Problem

The currently used program for pathway analysis gprofiler can't handle bacteria in general and applies only to isolates, i.e. a single species opposed to metatranscriptomics.

The Solution

All this software fits into the existing container without conflicts.

At least three independent analysis could be possible:

Required changes to workflow

  1. Addition of software (trivial)
  2. Achieve maximal flexibility: All parameters need to be optional, only exeption might be --metadata.
  3. New inputs for metatranscriptome samples (feature/pathway abundance): -- Pre-processed (optimally rRNA depleted) reads e.g. from nf-core/rnaseq v1.4+ (with parameters --remove_rRNA & --save_nonrRNA_reads), required for meta-pathway analysis -- Optional: databases (nucleotide, protein & utilities), default: automated download
  4. New inputs for paired metatranscriptome - metagenome samples (feature/pathway expression): -- Pre-processed metagenomics reads e.g. from nf-core/rnaseq v1.4+ -- Either a manifest file to link samples or same sample names but different folders

Conclusion

This would be a major increase in code / parameters and output. Pathway abundance (only metatranscriptome) would be the first step to implement, followed by addition of pathway expression analysis (RNA & DNA measures).

edit: added section "three independent analysis" edit2: nf-core/rnaseq v1.4 pre-processing is only valid for environmental samples! For host - microbiome studies the host sequences have to be removed too!

d4straub commented 4 years ago

Outdated...