Sample normalization - ChIP-Seq
Hello,
I am new here. I have started to analyse ChIP-Seq data. I have 2 conditions: High Fed and Control diets within different time points.
So, I have lots of BAM files for each sample. Now I want to do peak calling and finally motif prediction within the significant peaks.
However, I would need to somehow normalize my data to compare peaks.
Any idea howto to approach the problem ?
Should I do it before peak calling or after ? I heard something like downsampling but not sure howto use it in my case.
Any suggestions are most welcome.
I am new here. I have started to analyse ChIP-Seq data. I have 2 conditions: High Fed and Control diets within different time points.
So, I have lots of BAM files for each sample. Now I want to do peak calling and finally motif prediction within the significant peaks.
However, I would need to somehow normalize my data to compare peaks.
Any idea howto to approach the problem ?
Should I do it before peak calling or after ? I heard something like downsampling but not sure howto use it in my case.
Any suggestions are most welcome.