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I have a ChIP-seq data, four samples that each with a input data, just like above. And I want to estimate ChIP-seq background noise and normalize the ChIP data on the same level. If there is only one input, I can use deeptools Bamcompare to normalize. However, this data have four input files and a ChIP control, it really makes me confused and I don't konw how to process this data. Anyone can give me some advice? Thank you very much.
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input_control, chip_control, input_sample1, chip_sample1, input_sample2, chip_sample2, input_sample3, chip_sample3
I have a ChIP-seq data, four samples that each with a input data, just like above. And I want to estimate ChIP-seq background noise and normalize the ChIP data on the same level. If there is only one input, I can use deeptools Bamcompare to normalize. However, this data have four input files and a ChIP control, it really makes me confused and I don't konw how to process this data. Anyone can give me some advice? Thank you very much.
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