I saw some papers on DNA methylation using BS-seq,now I meet some questions on DNA methylation when working with the BS-seq data:
1)first,what is the minimum required threshold of percent methylation at a site to dedine a methylcytosine,I want to use 40%,but I don't know if it was appropriate;
2)second,somebody mentioned methylation genes in some papers,so how to define a methylated genes,what the criteria is ? Because you know,the raw results of BS-seq is the methylation level at each site,and both of the methylation sites and the C are not even between a gene;
3)Also,I want to know how to define a differentially methylated region(DMR),this question is in fact the same as my second one because of the uneven methylation cytosine in the chromosomes;and in plant how long (300 bp?) to set the length of DMR in your experiences
Thanks for your time!
Best wishes,
1)first,what is the minimum required threshold of percent methylation at a site to dedine a methylcytosine,I want to use 40%,but I don't know if it was appropriate;
2)second,somebody mentioned methylation genes in some papers,so how to define a methylated genes,what the criteria is ? Because you know,the raw results of BS-seq is the methylation level at each site,and both of the methylation sites and the C are not even between a gene;
3)Also,I want to know how to define a differentially methylated region(DMR),this question is in fact the same as my second one because of the uneven methylation cytosine in the chromosomes;and in plant how long (300 bp?) to set the length of DMR in your experiences
Thanks for your time!
Best wishes,
Comment