Chip-Seq Analisis

[suludana]

I am analyzing my first data of Chip-Seq (with the antibody H4K16Ac) using Partek.

In the initial step of detecting peaks I obtained a lot of peaks for some of the samples (100.000 – 200.000) and of course, then, I obtained large lists of associated genes. How can I do to filter these data? The control (not IP) is not enough to reduce substantially these values.

Can I filter by the number of reads in each peak? In this case which would be the optimal value?

Thanks!

[snetmcom]

These are the same issues you get with every Chip seq experiment.
Focus on a few genes and adjust some of the filters, then see how it plays with the rest of the data.

[suludana]

Do you think it would be correct to adjust filters based on some housekeeping genes?