Chipseq with three replicates

Question

[maryamforoozani16]

Hello , I did chip experiment with three replicates for two conditions ( normal condition(C) and phosphate deficiency condition (P)) on Rice genome. I tried to find differential regions from two conditions. - My replicates have the different depth. Do you think this is the reasons that I could not find high correlation between my C samples?

Answer 1

[Devon Ryan]

Possibly, or perhaps you just have a difference in IP efficiency or something else. Have a look at the data in IGV and use plotFingerprint from deepTools.

[maryamforoozani16]

Thanks Devon for your suggestion. I did plot fingerprint and it seems in one of my replicates I could not get a good ChIP signal. It helps me a lot. Thanks