Inconsistency between biological replicates

[Nicholas_]

Hello,

So i am relatively new to the whole chip-seq analysis.

I have 2 different biological replicates for the same protein and i am using 2 controls as well.

For my peak analysis i am using the new version of Cis Genome, with a cutoff of 5, a bin size of 33 and no poisson.

And here is where i have the problem. I have uploaded my initial before peak calling BED files in the Genome Browser in order to visualise them and see how they worked. My BED files look very similar before peak calling but when i perform peak calling the consistency is very very low...around 50%

What could go wrong? Is it my settings? I am trying to figure it out for weeks but i can't. Maybe i am too stupid! Please help!!! Any suggestions would be apprecited!

Thnx
Nick

[tir_al]

Have you tried looking at the duplication rate of your libraries? Although the distributions might look the same in the browser, the high duplication rate in one sample can really mess up the peak calling.

You can check the duplication rates very easily using the excellent FastQC app.