Tracks and Tables

This section contains summary metrics for each sample as well as links to exported files. The summary table below contains the following metrics. It is also available as csv file.

• sampleName: Name of the sample
• *_num (* can be 'sites' or a region type): Number of sites or regions with coverage in the sample
• **_numSitesMean (** is any region type): Mean number of sites in a region
• **_numSitesMedian (** is any region type): Median number of sites in a region
• **_numSites2,5,10,20: Number of regions with at least 2,5,10,20 sites with valid methylation measurements

Bed files for each sample contain the locations of methylation sites and regions the methylation level (in the score column). The following table links to the files. The files can be quite large in size, so you might want to consider using the "save as" option instead of opening the links directly.

Track Hub data was generated for export to various genome browsers. Note that you need a server that is capable of serving the tracks to the genome browser via URL. Below, instructions are provided to view the tracks in the UCSC genome browser. Of course the files can also be viewed in other browsers such as the Ensembl genome browser.

1. Convert the bed/bedGraph files contained in the bed/bedGraph directories (see table below) attached to this report. You can use the UCSC tool bedTobigBed/bedGraphTobigWig for this task. More information (e.g. where to obtain the tool) on how to convert can be found here. Make sure the resulting bigBed/bigWig files are moved to the corresponding UCSC track hub directory (see table(s) below).
2. Make sure you are viewing this report via the internet and not locally (simply look at the URL in the address line of your browser). If this is not the case, copy the files belonging to this report to a directory which is accessible via the internet and enter the corresponding URL in your browser. If you don't want to copy the entire report, it suffices to copy the track hub directories (see table(s) below).
3. Make sure the hg19 subdirectories in the track hub directory (for its location be referred to the table(s) below) contain all the required bigBed/bigWig files
4. Go to the UCSC hub connection website to the "My Hubs" tab and add the web-URL of the hub.txt file in the directory you just copied. Hint: You can use the copy link functionality of your browser (right mouse click) on the track hub txt column in the table(s) below. Don't forget to click on "Load Selected Hubs".
5. Make sure you are looking at the correct genome (hg19). The loaded hubs should now appear below the browsing window where you can modify their display settings.

More information on UCSC track hubs can be found here. Below, you find table(s) containing the directory names for the bed/bedGraph and track hub directories for all exported data, site and region types.

bigBed

This report was generated on 2017-12-19 by RnBeads version 1.11.3.