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Low mapping efficiency of WGBS data for DNA methylation

Epigenetics WGBS DNA Methylation

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#1 Naveed Jhamat

Naveed Jhamat


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Posted 15 November 2016 - 02:37 AM

I am analysing WGBS data (Illumina Hiseq) of Bovine FAT tissues for differential methylation. I used TrimGalore for adaptor removal and qulity check for the the pilot sample . All the adoptors were removed and quality was good (both survived paired end reads 98%). Then I used Bismark for unique alignment to the Bisulfite converted reference genome and I got 57.8% mapping efficiency.
I want to ask wether 57.8% mapping efficiency is good to proceed further ? What is gold standard for mapping efficiency in WGBS? Please guide me.

Naveed Jhamat.

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