Comments (2)
Hi there, naked DNA sequencing isn't necessary. Data from He. et al (2014) (Shirley Liu's lab) Naked DNA was used to determine DNase I cutting preference for all 6-mers, and this data is here
However, for ATAC-seq data if you wanted to normalise against ATAC-seq insertion bias then you'd need a dataset to determine this from. A common method is to use all the cuts outside the peaks but the better method is to use Naked DNA for this.
You can look at dnase_bias_estimator.py on how to calculate your own bias file, and then you use this fie in dnase_average_profile.py
or dnase_to_javatreeview.pywith the "--bias-file" command.
If you look in the code, what is actually happening here is we're applying the formula developed in the original bias paper.
I never got around to correcting for bias during footprinting itself before I finished my PhD. I could look into doing this, though.
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Thanks for your reply!
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Related Issues (20)
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