Dynamic nucleosome identification

[hang zhao]

Dear Kaifu,

I am using danpos to identify dynamic nucleosomes in mouse ES cells as you did in your paper. I notice that you found ~5500 dynamic nucleosomes compared with EHP cells. However I used your data and found ~3800000 dynamic nucleosome according to the same cutoff 1e-50 in the paper. Is there something wrong? 

Thanks!

Hang

[simon holzinger]

Hi Hang, 

I don't know if I can help you, but there are several things worth mentioning: 

The original DANPOS paper used DANPOS in its first version. Current versions include an "FDR" value while the old version only had the pvalue. 

Pvalues in DANPOS heavily rely on the input coverage / normalization of reads. Maybe you used a different normalization? 

Best wishes 

Simon