In methylkit how is average conversion rate calculated or formaula for calculation average conversion rates?

[Laxman Iyer]

My question is whether average conversion rates given by methylkit = bisulfite conversion rate?
here is the output:
total otherC considered (>95% C+T): 28609
average conversion rate = 2.99096846542875
total otherC considered (Forward) (>95% C+T): 14623
average conversion rate (Forward) = 2.87848191283719
total otherC considered (Reverse) (>95% C+T): 13986
average conversion rate (Reverse) = 3.10857827942463

Since i wanted to calculate bisulfite conversion rate? please help me with a suitable reply.

[Altuna Akalin]

This is one way estimating conversion rate, a more accurate conversion rate can be obtained via spike-ins in the experiment but many papers report this or similar values as bisulfite conversion rate, and general idea of conversion rate has been explained before:

https://groups.google.com/d/msg/methylkit_discussion/A5_LeS8y3Ks/lFect-XFJ3kJ

Please consider using search function in the forum, you will find that many questions are already answered in the forum.

Best,

Altuna

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[Laxman Iyer]

So what i wanted to know is that can i use directly the average conversion rate as bisulphite conversion rate since i have only the alignment files and need to submit the report within 2days by insilico bisulfite conversion rates. So whether i can use it directly for my calculation is that fine?

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Regards,
Laxman Iyer

[Altuna Akalin]

yes, some report  that value as conversion rate