BiQ Analyzer Diagrams - DNA methylation diagrams made simple

Methylation data is often reported in the form of so-called lollipop diagrams. Here we provide an easy-to-use web tool to generate publication-quality lollipop diagrams (and a second diagram type) from sequence-specific methylation data. Thereby, this web service supplements the BiQ Analyzer tool for methylation analysis by bisulfite sequencing with a diagram generator that can be applied to pre-analyzed DNA methylation data.

Format of input Uncompressed (see example) Compressed (see example)	Diagram options Sequence sorting (1st diagram) Proportional distances (1st diagram) Lollipops (rather than beads) (1st diagram) Include legend (2nd diagram)
Graphics options Transparent background Image resolution: Line break position: Generate image as: PNG or as: SVG	Color options (in hexadecimal format) Color of unmethylated CpGs: Color of methylated CpGs: Color of missing values:

WARNING: the input must exactly resemble the format specified by one of the two examples linked above (including a tab after the sequence name), otherwise the program is unlikely to work properly. If you copy and paste data from the HTML documentation file generated by BiQ Analyzer ("Results in Machine-readable Format" section) no problems should occur. But Mac users beware: The Safari browser seems to have the bad habit of replacing tabs by variable numbers of spaces, which breaks things as well. In that case you can either open the html file directly in a text editor and copy from there or you use a different web browser.

Download BiQ Analyzer Diagrams

If you have to generate DNA methylation diagrams regularly or on a large scale, you may want to download BiQ Analyzer Diagrams for local use. The program is command line based and requires nothing but a recent Java version to run.

The program can be downloaded from here, provided that you accept the BiQ Analyzer Licence Agreement (free for non-commercial use, no warranty, no redistribution). If you would like to use the diagram generation in your own software, please feel free to contact the developers and ask for the source code.