Sequencing of bisulfite-treated deoxyribonucleic acid DNA is the gold standard for base resolution mapping of DNA-methylation 3—5. The Software and any copies shall be destroyed. Any commercial use of the software, including modified versions not developed in collaboration with MPII, is strictly forbidden please contact MPII for commercial a license. It includes a project summary table, presenting the most crucial information about each read batch, the project-level heat maps visualizing average modification levels and locus-wide bar charts dynamically generated for each selected read batch. For every type of analysis BiQ HiMod takes into account all potential modifications and summarizes the information accordingly.

Therefore, when the bisulfite treatment fails to convert unmethylated Cs, methylation will be overestimated.

Correspondence may also be addressed to Pavlo Lutsik. A quantitative assessment of the relative abundances of different modifications depends on the comparison of two independent sequencing results.

Non-commercial users can download BiQ Analyzer free of charge from http: In an easy-to-use manner, the tool helps the user to import the sequence files from the sequencer, to align them, to exclude or correct critical sequences, to document the experiment, to perform basic statistics and to produce publication-quality diagrams.

BiQ Analyzer – a software tool for DNA methylation analysis

Wait for the download to complete and double-click on the downloaded file to start BiQ Analyzer’s installer. Final results can be exported as tables, figures, alignments and genome browser tracks see Supplementary text ibq a detailed list.

Most of the plotting parameters, including the flexible color scheme, are fully user-adjustable. This is a necessary prerequisite for the second generation of DNA methylation databases that will validate data quality and that will accept direct submissions from the public.

Quantitative sequencing of 5-methylcytosine and 5-hydroxymethylcytosine at single-base resolution. DNA methylation is widely recognized as a key epigenetic mechanism playing a crucial role in development and disease 12. MPII is not liable to the damage caused by modified znalyzer.

Sequencing the sixth base 5-hydroxymethylcytosine: Finally, the summarized data in bedGraph format can be loaded into our in-house genome-wide DNA methylation data analysis package RnBeads http: End-to-end support of the analysis bjq In such a setting BiQ HiMod requires the direct sequencing output to be demultiplexed using available third-party tools.

BiQ Analyzer – a software tool for DNA methylation analysis

If you have any problems or suggestions, please write an ahalyzer to biq-analyzer bioproject. In order to download BiQ Analyzer, please fill out the form below only one field is mandatoryselect the operating system Windows or MacOS, Linux, Unixtick the box indicating acceptance of the licence agreement and press the Download button.

BiQ Analyzer is a software tool for easy visualization and quality control of DNA methylation data from bisulfite sequencing. Applicable Law and Court of Jurisdiction This Agreement is made and shall be construed in accordance with the laws of Germany. Moreover, the statistical significance of the observed variation should be tested.

Emphasis is put on quality control: First, BiQ Analyzer imports sequence files directly from the sequencer without the need for any manual intervention and assists the user with all steps of alignment and quality control.

BiQ Analyzer: visualization and quality control for DNA methylation data from bisulfite sequencing.

Finally, BiQ Analyzer provides an interactive graphical interface that guides the user through quality control and gives continuous feedback on problematic sequences. The tool currently supports four experimental assays and can be easily extended to include the upcoming methods. In several steps, the user is guided from the import of sequences, across several phases of quality control and multiple sequence alignment, to a questionnaire documenting the experiment.

In vertebrates, it almost exclusively affects the C5 position of cytosines that belong to CpG dinucleotides i. Recently, oxidized derivatives of 5-methylcytosine 5mC were identified that are assumed to have important biological function 6.

We then applied BiQ HiMod to reprocess the earlier published oxBS-seq data set obtained by sequencing of repetitive elements in two types of mouse ES cells The tool is freely available as a stand-alone installation package from http: Email alerts New issue alert. annalyzer

Open in a separate window. Sequencing of bisulfite-treated deoxyribonucleic acid DNA is the gold standard for base resolution mapping of DNA-methylation 3—5. Please download the most recent Java version from http: Here we present BiQ Analyzer HiMod, a user-friendly software tool for sequence alignment, quality control and initial analysis of locus-specific DNA modification data.