Mouse Chipseq Depth of seq

Question

[kanwarjag]

I was wondering can we use MI-seq for Mouse genome ChIP-seq? I believe it will not represent the complete genome. However My dilemma is we have already started sequencing on Miseq and have 20 million reads. Is there any alternative to rescue this data or should I seq more on MIseq?

Thanks.

[Ming Tommy Tang]

10 million unique mapped reads will be sufficient for transcription factors. I actually see many published data with 5 million reads....

Answer 1

[Devon Ryan]

20 million reads could well be adequate, depending on what you're pulling down. See for example this paper.