> For the complete documentation index, see [llms.txt](https://help.multiomics.illumina.com/llms.txt). Markdown versions of documentation pages are available by appending `.md` to page URLs; this page is available as [Markdown](https://help.multiomics.illumina.com/icm/reference/list-of-analysis-tasks-by-data-type/5-base-dna-methylation.md). # 5-base DNA Methylation ## Methylation CpGs Count Matrix Examples of methylation CpGs count matrix are 5-base Methylation, Filtered counts. Analysis tasks that can be invoked from the methylation count matrix are listed below. | Task Menu Section | Analysis Task Name | | -------------------- | ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- | | Annotation/Metadata | | | QA/QC | | | Pre-analysis tools | | | Filtering | | | Statistics | | | Exploratory analysis | | | Region analysis | | | Conversion | | ## Methylation Regions Count Matrix For regional methylation data, such as those generated from the [Get Regional Methylation](https://help.multiomics.illumina.com/icm/analyses/analysis-functionality/task-menu/region-analysis/get-regional-methylation) task, the following tasks can be initiated from the regions count matrix. | Task Menu Section | Analysis Task Name | | ------------------------- | --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- | | Annotation/Metadata | | | QA/QC | | | Pre-analysis tools | | | Statistics | | | Exploratory analysis | | | Region analysis | | | Motif detection | | | Biological interpretation | | | Conversion | | ## PCA Analysis tasks that can be invoked from PCA data node are listed below. | Task Menu Section | Analysis Task Name | | -------------------- | ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- | | Annotation/Metadata | | | Batch removal | | | Statistics | | | Exploratory analysis | | | Conversion | | ## Differential Methylation Analysis Result Analysis tasks that can be invoked from differential methylated regions analysis (e.g., DSS, Detect differential methylation) are listed below. | Task Menu Section | Analysis Task Name | | ------------------------- | ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ | | QA/QC | | | Filtering | | | Statistics | | | Exploratory analysis | | | Region analysis | | | Motif detection | | | Biological interpretation | | ## DNA Variants | Task Menu Section | Analysis Task Name | | -------------------- | ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ | | Exploratory analysis | | | Variant analysis | | ## Annotated Features Examples of annotated features are annotated methylation regions, and annotated variants. Depends on the feature type, different analysis tasks can be invoked from the annoated features data. For example, for annotated methylation regions generated from Get Regional Methylation task, analysis that can be invoked from this annotated features data are similar to the [Methylation Regions Count Matrix](#methylation-regions-count-matrix). For annotated variants, analysis that can be invoked from this data are similar to the [DNA variants](#dna-variants). Analysis task that is common across the feature types is listed below. | Task Menu Section | Analysis Task Name | | ----------------------- | ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- | | Combine multiomics data | | --- # Agent Instructions This documentation is published with GitBook. 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