I'm a student and I do research on the Y chromosome.
I converted a lot of extracted DNA with the bisulphate Epitect Bisulphate kit.
After the conversion I did a NPCR and inserted the fragments in a plasmid.
I cloned them in E. coli cell and finally I did a sequencing with the purifate plasmid DNA.
Not all the unmethylated C were converted into U. Now I need to calculate the conversion ratio.
But I don't know if I have to calculate it for all the clones together or all seperatly.
for example if i have three clones and in the sequence there are 32 C that should be converted into T.
clone 1: still has 1 C
clone 2: still has 2 C
clone 3: hasn't a C
the conversion ratio of the clones seperatly are than:
clone 1: 31/32 = 97%
clone 2: 30/32 = 94%
clone 3: 32/32 = 100%
or for all together: (96-3)/96 = 97%
Which way do I need to use?