MEDIPS quality control
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@liujie_1914-6788
Last seen 7.2 years ago

Hello, when I do quality controls with data derived from methylated DNA binding domain sequencing(human genome),how big maxTruCor , maxEstCor, enrichment.score.relH, enrichment.score.GoGe should be so that I can confirm my experiment is successful. In other words, what’s the minimum of maxTruCor , maxEstCor, enrichment.score.relH and enrichment.score.GoGe? Thank you very much.

process medips • 1.1k views
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Lukas Chavez ▴ 570
@lukas-chavez-5781
Last seen 3.8 years ago
USA/La Jolla/UCSD

Hello,

please excuse my terribly late response, but I missed this question due to transition to this bioconductor support environment.

Indeed, for both quality controls (saturation analysis and CpG enrichment) there is no 'traffic light' like output indicating if the results are good ('green') or bad ('red'). However, by visual inspection of the saturation curve you should be able to judge, if your sequencing depth is sufficient for starting further analyses or if you are far away from saturation. Similarly, the values for "enrichment.score.relH" or "enrichment.score.GoGe" will indicate, if you have a CpG enrichment in you MeDIP/MBD data compared to the reference genome or compared to Input data. You might want to compare your results to some reference results, for examlple in http://www.ncbi.nlm.nih.gov/pubmed/23408899 (Table S1, S2) we have given concrete numbers for CpG enrichment scores which we consider as sufficiently good.

 

All the best,

Lukas

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