From idat Illumina Infinium MethylationEPIC to CNV analysis for homo/hetero-zigous deletion
My group works on cancer and we have difficulty on a little part of our last project about malignant pleuric mesothelioma.
I’m looking for help in the analysis of .idat from genome-wide DNA methylation profiles obtained via Illumina Infinium MethylationEPIC BeadChips. In particular, I already have CNV plot useful to visualize gene loss or gain, but I am looking for a specif tool to identify automatically homozygous / heterozygous deletions or chromothripsis, with error estimation (related to the quality of DNA sample) and using an adequate threshold of statistical significance.
I would really appreciate your kind help to solve this quest.
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