Hii everyone.
So, I have obtained the DNase-Seq prediction values from AG, for some sequence, and peak values are obtained for each nucleotide. I was wondering if you guys could help me interpret those signals, as in, is there any threshold value, or what are the values that we should be considering for the DNase-seq?
looking forward to a fulfilling response.
Thankyou.
Regards.
Thanks for reaching out. The base resolution signal in DNase-seq represents the normalised number of reads aligning at that position. Note that this signal at the high resolution is driven to a large degree by the DNase cut bias. To interpret the signal more from the accessible / non-accessible region perspective, we recommend looking at the data at the lower resolution (for example by coarse-graining the data). More broadly, we’d suggest reusing strategies for interpreting the raw DNase coverage data and then applying similar principles to model predictions. Regarding the ‘threshold values’, a peak calling algorithm could be employed, similarly to how people interpret raw DNase data.