# Visualize methylation at each locus Partek Genomics Suite enables you to visualize each probe and compare the methylation between the groups at a single CpG site level. * Right click row 5\_. SBNO2\_ in the *LCLs\_vs\_B\_Cells\_CpG\_Islands* spreadsheet * Select **Browse to Location** from the pop-up menu ![](/files/Lpp2nHVOKwaNR01kSdyd) Figure 1. Browsing to location from spreadsheet with differentially expressed genes The *Chromosome View* tab will open, zoomed in to the selected CpG locus in SBNO2 (Figure 2). ![](/files/JQIikBqA25FeqWpxMtDS) Figure 2. Viewing location in Genome Viewer The *Chromosome View* visualization is composed of a series of tracks corresponding to annotation files and data files. * *RefSeq Transcripts 2017-05-02 (hg19) (+)*: transcripts coded by the positive strand * *RefSeq Transcripts 2017-05-02 (hg19) (-)*: transcripts coded by the negative strand * *Regions*: by default, difference in methylation (M-value) between the groups * *Heatmap (1/mvalue)*: M values for all the samples * *Barchart (Methylation)*: methylation level in M value of the selected sample (to select a sample, click on a heat map) * *Heatmap (Methylation Tutorial)*: Beta values for all the samples * *Barchart (Methylation)*: methylation level in Beta value of the selected sample (to select a sample, click on a heat map) * *Cytoband*: cytobands of the current chromosome * *Genomic Label*: coordinates on the current chromosome To modify a track, select it in the *Tracks* panel to bring up its configuration options panel below the *Tracks* panel. Let's modify a few tracks to improve our visualization of the data. * Select the *Regions* track, opens to *Profile* tab * Select *Color* tab * Set *Color bars by* to **Difference (LCLs vs. B cells) (Description)** * Select **Apply** to change This will color regions by up or down methylated. * Select the *Heatmap (1/mvalue)* * Select **Remove Track** * Select *Bar Chart (Methylation)* located directly below the *Regions* track * Select **Remove Track** We can now more clearly see the Difference in M values for the region in the *Regions* track, the heatmap of beta values in the *Heatmap* track, and the beta value for the loci of the selected sample in the *Bar Chart* track. * Select a sample on the heatmap to view its beta value in the *Bar Chart* track (Figure 3) ![](/files/lJhbEz0yKXvD0K2JdT5u) Figure 3. Modify the tracks of the Genome Viewer to facilitate visual analysis The **New Track** button allows new tracks to be added to the viewer, while the **Remove Track** button removes the selected track from the viewer. Tracks can be reordered by selecting a track in the *Tracks* panel and dragging it up or down to move it in the list. In the *Chromosome View*, select (![](/files/JwK9lqde4w6G9QFFS3hB)) for selection mode and (![](/files/RTTRKf8IR5I9PaUvO1L6)) for navigation mode. In navigation mode, left-click and draw a box on any track to zoom in. All tracks are synced and will zoom together. Zooming can also be controlled using the interface in the lower right-hand corner of the tab (![](/files/zRwR3vGNay17qbMSOyV3)). View can be reset to the whole chromosome level using reset zoom (![](/files/zJlhyODVg2UIrUasNPZ9)). Searching for a gene or transcript in the position box will also zoom directly to its location. The available tracks can be supplemented with a special annotation file that can be built using a UCSC annotation file as the basis. Building and viewing the UCSC annotation file is available as an optional section of the tutorial, [Optional: Add UCSC CpG island annotations](/partek/partek-genomics-suite/tutorials/differential-methylation-analysis/optional-add-ucsc-cpg-island-annotations.md). ## Additional Assistance If you need additional assistance, please visit [our support page](http://www.partek.com/support) to submit a help ticket or find phone numbers for regional support. --- # Agent Instructions: Querying This Documentation If you need additional information that is not directly available in this page, you can query the documentation dynamically by asking a question. Perform an HTTP GET request on the current page URL with the `ask` query parameter: ``` GET https://help.multiomics.illumina.com/partek/partek-genomics-suite/tutorials/differential-methylation-analysis/visualize-methylation-at-each-locus.md?ask= ``` The question should be specific, self-contained, and written in natural language. The response will contain a direct answer to the question and relevant excerpts and sources from the documentation. Use this mechanism when the answer is not explicitly present in the current page, you need clarification or additional context, or you want to retrieve related documentation sections.