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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.