This is the community page for the EpiExplorer project.
Here you can tell us how can we make EpiExplorer more useful to you. Feel free to suggest new features, datasets, visualizations or vote for features suggested by other users.
Bug reports are also eagerly anticipated, especially on Friday night
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Dear Konstantin, I have a related question. I have been exporing the original methylation files and was wondering which thresholds does EpiExplorer use for read coverage and percentage of reads with methylation. In UCSC they recommend requiring at least 10 reads and they assign colors depending on what fraction of the reads is found to be methylated.
For example, a profile plot showing 5,10,15,11,6 for the overlap of set of regions with CGIs will show that the 5'end overlaps in 5%, the 1/4 point overlaps in 10%, the middle point overlaps in 15% etc and would be indicative that the middle of the regions tend to be more overlapping with CGIs than the ends.
Would it be possible to also get the rat genome (rn5) availlable?
If you are planning a larger rat project we would certainly consider contributing. If this is the case, please contact our corresponding authors with more details (http://genomebiology.com/2012/13/10/R96). Otherwise, in order to be worth setting things up, we would need serious user interest in this genome that we have not yet observed.
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I am comparing a bed of exons against the corresponding full-genes bed file. By looking at "DNA methylation (ENCODE)" I can see higher bars for full-genes (e.g. 75% unmethylated for genes compared to 5% unmethylated for exons).
Below, it can be read:
Chart description: The bar chart visualizes the percentage of regions in the selected region set that overlap with any of the listed genomic and epigenomic features on the x-axis.
Many thanks for EpiExplorer, it is really helpful,
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