I want to ask a general question and your valuable comments about my approach.
I am analyzing different ChIP-seq samples from different datasets under same conditions (i.e. : mcf7 er alpha control chip-seq under the same conditions). Some of them have really high peak numbers or contrarily very low compared to the numbers they should normally have.
I thought that I can compare my files with the same samples in ChIP-atlas. I see that also in ChIP-atlas, peak numbers could be really high. But I am not sure if it is making sense or not. If you could comment I would appreciate it. Thank you.