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6.5 years ago
ChIP
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Dear All,
I have 3 input samples, and I want to compare them and find out which is the best input to be used for peak calling. These samples have copy number variation.
Any help is appreciated.
Do you mean input controls, like, for ChIP-seq? Which programs have you already tried?
I'm not sure what you mean by copy number variation - the genome of everybody contains copy number variation to various extents. Did you mean copy number alterations or structural variants, as in, for example, changes between a germline DNA sample and that of a tumour that has a high level of genomic instability?
Hi,
Yes, I meant copy number alterations or structural variants, as in, for example, changes between a germline DNA sample and that of a tumour that has a high level of genomic instability.
Why doesn't your actual IP sample have the same CNVs as your input?
They have it, the point is should I use individual inputs or should I merge them all and use it.
You should use the individual inputs for each sample, assuming each of your IPs also has a corresponding input. More detail as to your experimental design would help people provide more definitive and well-reasoned answers.