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Old 12-18-2018, 07:53 AM   #1
Hedi86
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Location: Norway

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Cool RRBS mapping efficiency in CLC vs Bismark

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
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Old 12-20-2018, 06:51 AM   #2
Hedi86
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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.
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