how to do differential analysis for drug treated sample?

ay-lab / FitHiChIP

Statistically Significant loops from HiChIP data

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how to do differential analysis for drug treated sample? #65

Closed jiangshan529 closed 2 years ago

jiangshan529 commented 3 years ago

Hi, I am doing hichip analysis for TF1, and I add some drugs to see how the looping of TF1 will be influenced. Now I want to perform differential analysis to see which contacts changed after drug treatment. I only have chip-seq bam files for wild type TF1, and I don't have chip-seq bam files for drug treated TF1, so how should I set the parameter "ChIPAlignFileList"?

souryacs commented 3 years ago

Hi @jiangshan529 Sorry for such late response. Currently FitHiChIP needs representative ChIP-seq files from both categories. We are planning to implement one differential analysis version without any ChIP-seq input. We'll let you know. Meanwhile you can send us any suggestions or issues regarding the differential analysis. Thanks.