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Old 05-12-2015, 02:07 AM   #1
Location: UK

Join Date: Dec 2014
Posts: 42
Default number of CpGs covered

Hello All,

I have bisulfite sequencing data from the SeqCapEpi protocol from NimbleGen/Roch and I am beginning to analyse my data. I aligned using Bismark/bowtie2 and I'm using Unix and R to analyse the data. I would like to create a simple table to show the total number of reads and total number of CpGs and number of CpGs with at least 10x coverage. Please could you let me know how I would determine the number of CpGs in each of my samples?

Many thanks!
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