RRBS mapping efficiency in CLC vs Bismark

[Hedi86]

Hi

we are working with RRBS data from bull sperm samples. previously we used Bismark mapper for pig data and the results were very good (around 60% mapping efficiency). however for bull data we used different kit to prepare the libraries and this time we got only around 24% unique mapping efficiency in bismark using default settings. interestingly we got around 75% mapping efficiency for the same dataset using CLC (CLC has developed a Genomics Workbench for detecting DNA methylation, recently).

so aim wondering why we get such a big differences ? anybody has worked with new pipline in CLC ? and how CLC does the mapping ? do you think that 75% mapping efficiency is unique mapping?

thank you for your help

[Hedi86]

we contacted CLC and they confirmed that mapping efficiency in CLC is unique and un unique mapping, thats why we ended up with 75%. they showed us how to extract only unique mapping and the results was very similar to Bismark.