Hello all,
I plan to perform some ChIP-Seq and Bisulfite sequencing. Does anyone have any idea how much coverage is "good" or "acceptable" for each of these methods and how many replicates are required?
My issue is my organism's genome is over 200 Mb. If I want just 1X coverage using GAIIx, it would itself require 1.2 entire flow-cells under ideal conditions. Then there need to be replicates and controls and the cost just explodes.
I know some groups have started to use multiplexing for genotyping and ChIP-Seq. But that is at the cost of coverage. So, something ~ 0.1X coverage in bisulfite sequencing or ChIP-Seq...is that good?
Any thoughts welcome
Thanks,
Flobpf
I plan to perform some ChIP-Seq and Bisulfite sequencing. Does anyone have any idea how much coverage is "good" or "acceptable" for each of these methods and how many replicates are required?
My issue is my organism's genome is over 200 Mb. If I want just 1X coverage using GAIIx, it would itself require 1.2 entire flow-cells under ideal conditions. Then there need to be replicates and controls and the cost just explodes.
I know some groups have started to use multiplexing for genotyping and ChIP-Seq. But that is at the cost of coverage. So, something ~ 0.1X coverage in bisulfite sequencing or ChIP-Seq...is that good?
Any thoughts welcome
Thanks,
Flobpf
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