Hello
im trying to calculate the percentage of covered CpG sites in my RRBS library and compare it with total CpG sites in reference genome. i got splitting report from Bismark (see bellow)
q1- could i say CpG sites in my RRBS library are equal to number of Total methylated C's in CpG context + number of Total C to T conversions in CpG context (around 19 million) ? if No how i can find total CpG sites in RRBS library?
q2- i downloaded pig CGI annotation and counted all CpG sites but the total was around 2 million. sound very low for me. how i can find the actual number of CpG sites in reference genome?
q3- is there a way to determine CpG sites per chromosome and compare it with CpG sites in each chromosome of reference genome?
Final Cytosine Methylation Report
=================================
Total number of C's analysed: 141645338
Total methylated C's in CpG context: 7904886
Total methylated C's in CHG context: 50683
Total methylated C's in CHH context: 107717
Total C to T conversions in CpG context: 12298571
Total C to T conversions in CHG context: 35912924
Total C to T conversions in CHH context: 85370557
im trying to calculate the percentage of covered CpG sites in my RRBS library and compare it with total CpG sites in reference genome. i got splitting report from Bismark (see bellow)
q1- could i say CpG sites in my RRBS library are equal to number of Total methylated C's in CpG context + number of Total C to T conversions in CpG context (around 19 million) ? if No how i can find total CpG sites in RRBS library?
q2- i downloaded pig CGI annotation and counted all CpG sites but the total was around 2 million. sound very low for me. how i can find the actual number of CpG sites in reference genome?
q3- is there a way to determine CpG sites per chromosome and compare it with CpG sites in each chromosome of reference genome?
Final Cytosine Methylation Report
=================================
Total number of C's analysed: 141645338
Total methylated C's in CpG context: 7904886
Total methylated C's in CHG context: 50683
Total methylated C's in CHH context: 107717
Total C to T conversions in CpG context: 12298571
Total C to T conversions in CHG context: 35912924
Total C to T conversions in CHH context: 85370557
Comment