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      "source": "mobileRNA.Rmd",
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      "title": "mobileRNA: Investigate the RNA mobilome & population-scale changes.",
      "author": "Katie Jeynes-Cupper, Marco Catoni",
      "engine": "knitr::rmarkdown",
      "headings": [
        "Introduction",
        "Approach",
        "sRNA Analysis",
        "Information on the sRNA cluster:",
        "Information on each sample replicate:",
        "For mRNA Analysis",
        "Information on the mRNA:",
        "Installation",
        "Installing OS Dependencies",
        "Example Data",
        "Example Workflow: Locating the sRNA Mobilome",
        "Quick Start",
        "Merging Genome Assemblies",
        "Merging Genome Annotations",
        "Alignment",
        "Import Pre-Processed Data into R",
        "Import Example Data",
        "Identify Potential Mobile sRNA clusters",
        "Advancing the Analysis",
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        "PCA",
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        "Define the consensus dicercall",
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        "Functional analysis of gained sRNA populations",
        "Mobile sRNA Analysis",
        "Heatmap plots to represent mobile molecules",
        "Functional analysis of putative mobile sRNA clusters",
        "Add genomic attributes to sRNA clusters",
        "Summarise sRNA cluster overlaps with genomic features",
        "Retrieve RNA sequence from mobile sRNA clusters",
        "Appendix",
        "Manual sRNA Alignment Pipeline",
        "Step 1 - De novo sRNA analysis",
        "Step 2 - Build sRNA cluster list",
        "Step 3 - sRNA clustering",
        "Manual mRNA Alignment pipeline",
        "Single-End Sequencing Reads",
        "Pair-End Sequencing Reads",
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