Can I downsize ChIP-seq data for ChIP-ed samples

Question

[Insect_gmx]

I've similar sequencing depth of roughly 50million bp for my TF-ChIP. I work with non-model organism with a genome size of roughly 300Mb. I realised that my ChIP-seq reads are about 50million bp (37bp, PE) and so are my inputs. I cannot re-sequence my inputs. Is it advisable to downsize by ChIP-ed samples to 30/40million bp?

[rfran010]

It's unclear to me why you think you need to down-sample. It sounds like you have similar read depths, which should be a good thing.

If you are concerned that the INPUT is not deep enough to give background relative to your TF-ChIP, I think that depends more on library complexity. INPUT should not be bottle necked, while TF-ChIP should be less complex. If this is satisfied, then I think the ChIP and inputs are fine as is.