Suggestion on how to analysis the ChIP-seq data

[yingsun-ucsd]

Hi, I have ChIP-seq data for one patient and one normal person as well as input for both of them (they run at different batch and each batch has a input). I am wondering what is the best way to do the analysis? I have some thinkings but think could get better idea from here.

1. compare patient and normal person respectively to the batch input to see if there is any different in between?

2. compare patient to combine controls (input and normal person together) to see if there are any differences?

Thanks.