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WGLab / DeepMod

DeepMod: a deep-learning tool for genomic-scale, strand-sensitive and single-nucleotide based detection of DNA modifications
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How to filter results? #37

Closed qiuyixmm closed 3 years ago

qiuyixmm commented 4 years ago

Hello , In my output file resulting from DeepMod, the methylation coverages of many sites were 0. So the mehylation percentage of these corresponding sites were also equal to 0. Should I remove these sites in which methylation coverages and mehylation percentage were both 0 ? In addition, it is necessary to filter real coverages and (or) methylation coverages to obtain more reliable methylated sites? If so, what are suitable cutoff values of real coverages and (or) methylation coverages that you would recommend ? Thanks!

liuqianhn commented 4 years ago

@qiuyixmm sorry for the late reply. In the output from DeepMod, there are some reference positions with 0 methylation coverage. It is not necessary to filter them if the coverage is large enough. According to the experience, you can set methylation percentages to 0.1 or 0.15 to have more reliable methylated sites, and it would be better if the coverage is higher, such as >10 or >20. The parameters depend on whether you can have enough methylated sites for further analysis. Please note that this is my experience, and I do not fully evaluate those parameters.

qiuyixmm commented 4 years ago

@liuqianhn whether these reference positions with 0 methylation coverage can be considered as the methylated sites or not ?

liuqianhn commented 4 years ago

If the total coverage is large enough, 0 methylation coverage means un-methylated sites.

liuqianhn commented 3 years ago

Closed due to no recent response. Feel free to reopen it if you need more help.