ENCODE peaks files - do I use the IDR files?

Question

[heskett]

Hi! I see that each ENCODE eCLIP peaks data file has a replicate 1, replicate 2, and an IDR file. Is the IDR file the correct file to use for downstream analysis? Or is that just metadata? thank you!

Answer 1

[jared.andrews07]

I'd recommend reading about the IDR method and its purpose. It's a method to identify concordance of peaks between replicates, so yes, that is likely the peakset you want.