SeqMonk tools for methylation analysis

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Presentation transcript:

SeqMonk tools for methylation analysis Simon Andrews simon.andrews@babraham.ac.uk @simon_Andrews 2016-11

SeqMonk

SeqMonk Data Model Conventional data (ChIP-Seq, RNA-Seq etc) Data is reads (BAM files etc) Strand indicates genomic strand BS-Seq and related data Data is methylation calls All ‘reads’ are 1bp in length Strand indicates meth state (+=meth -=unmeth) Original strand comes from the imported file

Raw Data Red = Meth Blue = Unmeth

Basic Movement Controls Move left right Drag bottom scrollbar Mouse scroll wheel Left/Right arrows Zoom In Drag a box and release Up arrow Zoom Out Right mouse button Down arrow Find a feature Edit > Find Feature Control+F Change chromosome Edit > Goto Position Drag a box in the genome view Data View Genome View Annotation Reads / Calls Quantitations Chromosome View

Raw Data Display View > Data Track Display

Quantitation Model Probe = Location to make a measurement ProbeSet = Collection of probes Quantitation associates a value with each probe for each data set. Define Probes > Quantitate Probes > Visualise

Probe Generation

Targeting Measurement Features Data > Define Probes > Feature Probe Generator

Targeting Measurement Fixed Windows Data > Define Probes > Running Window Generator

Targeting Measurement Fixed number of calls Data > Define Probes > Even Coverage Probe Generator

Targeting Measurement Fixed number of call positions Data > Define Probes > Read Position Probe Generator

Quantitation

Methylation Measurement Simple percentage of all calls Data > Quantitate Existing Probes > Difference Quantitation

Methylation Measurement More complex corrected measure Data > Quantitation Pipelines > Bisulphite methylation over features

Visualisation of quantitated methylation View > Data Track Display View > Set Data Zoom Level

Distributions Plots > Probe value histogram Plots > Cumulative Distribution Plot Plots > Beanplot

Comparisons Plots > Scatter plot Plot is interactive – mouse over a point for information Double click on a point to move there in the chromosome view

Trend Plots Plots > Quantitation Trend Plot

Clustering Plots > Hierarchical Clusters Correlation based (per probe normalised) Euclidean Plots > Hierarchical Clusters

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