methylation thresholds

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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.

Thanks again,

Federico

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11 aastat tagasi

Dear Federico,

In the summary methylation plot, we discussed, EpiExplorer takes into consideration only the methylation ratio. Keep in mind that this plot is only intended to provide intuition about the data.

In case, you want to inspect after you apply additional filters, I suggest you filter out your regions for number of CpGs (and/or coverage) and then you can inspect the details of the distribution of methylation ratios.

You can see an example here: http://www.slideshare.net/khalachev/step-by-step-guide-to-figure-1

slide 8

best,

Konstantin

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