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


Tell us how to make it better. We'll listen

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Federico Abascal 4 years ago • updated by Halachev 4 years ago 1

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.

Thanks again,

Federico


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Halachev 6 years ago 0
Add a profile how often certain positions inside the regions, such as the start, the middle and the end overlap with a certain property.

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.
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Anonymous 6 years ago 0

Allow more help bubbles?

For datasets information, tissues, plots, computations and others


One of those


http://craigsworks.com/projects/qtip/


http://craigsworks.com/projects/qtip2


http://www.vegabit.com/jquery_bubble_popup_v2/

Visualization
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Anonymous 5 years ago • updated by Halachev 4 years ago 0

Dear EpiExplorers,

Would it be possible to also get the rat genome (rn5) availlable?

Answer
Halachev 5 years ago

Dear user, 

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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Anonymous 2 years ago 0
I am a new user. I performed targeted bisulfite sequencing on 2 groups of samples and subsequently analyzed the data with Methylkit in R. My output file is a list of CpGs significantly differentially methylated between the 2 groups, with the 3 columns as requested by the EpiExplorer program (chr, start, end). My data is at single CpG level, thus start and end positions are exactly the same. This gives an error when uploading the file: "

Error: Invalid format at line 0. chromosome end(843641) should be larger than chromosome start (843641)"



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Anonymous 4 years ago • updated by Mario Saare 4 years ago 2
Great tool. Any chance to get an export function for the matched control regions that are generated by epiexplorer?


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Anonymous 5 years ago • updated by Halachev 4 years ago 1
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Anonymous 4 years ago • updated by Federico Abascal 4 years ago 3

Dear colleagues,

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.

And this is what I do not understand. The plot suggests more methylation on exons, but the chart description refers to percentages of regions that overlap with a given epigenomic feature. Then, if an exon intersects with a methylated region, then the corresponding gene should intersect too. What am I missing here?


Many thanks for EpiExplorer, it is really helpful,

Best,

Federico