SeqMonk Tools for Methylation Analysis Overview

Explore the features and functionalities of SeqMonk for methylation analysis, including data model, raw data visualization, movement controls, quantitation models, probe generation, and targeting measurement methods.

• Methylation analysis
• SeqMonk tools
• Data model
• Raw data display
• Probe generation

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1. SeqMonk tools for methylation analysis Simon Andrews simon.andrews@babraham.ac.uk @simon_Andrews 2016-11 1

2. SeqMonk 2

3. 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 3

4. Raw Data Red = Meth Blue = Unmeth 4

5. 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 5

6. Raw Data Display View > Data Track Display 6

7. 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 7

8. Probe Generation 8

9. Targeting Measurement Features Data > Define Probes > Feature Probe Generator 9

10. Targeting Measurement Fixed Windows Data > Define Probes > Running Window Generator 10

11. Targeting Measurement Fixed number of calls Data > Define Probes > Even Coverage Probe Generator 11

12. Targeting Measurement Fixed number of call positions Data > Define Probes > Read Position Probe Generator 12

13. Quantitation 13

14. Methylation Measurement Simple percentage of all calls Data > Quantitate Existing Probes > Difference Quantitation 14

15. Methylation Measurement More complex corrected measure Data > Quantitation Pipelines > Bisulphite methylation over features 15

16. Visualisation of quantitated methylation View > Data Track Display View > Set Data Zoom Level 16

17. Distributions Plots > Probe value histogram Plots > Cumulative Distribution Plot Plots > Beanplot 17

18. 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 18

19. Trend Plots Plots > Quantitation Trend Plot 19

20. Clustering Correlation based (per probe normalised) Euclidean Plots > Hierarchical Clusters 20