How to calculate the correlation between two ChIP-seq INPUT datasets?

Question

[Zee_S]

Hello everyone,

I have a very general question.

I have two Input datasets from two ChiP-seq experiments. How does one calculate the correlation between two input samples by taking into account the following:

(i) Normalize for library size and sequencing depth.

For two treated IP datasets, its possible to calculate enrichment over input and then correlate the two enrichment files.

But what approach can one take for two inputs that need to be compared to each other?

Thank a lot for your suggestions!

[ATpoint]

You could use multiBamSummary from deeptools to compare the two files. It takes sequencing depth into account, optionally binning the genome prior to file-to-file comparison. The putput can be used to calculate, e.g. the Pearson Correlation for counts per bin across the two files.