Quantifying Peak Height Difference in ATAC-seq

Quantifying Peak Height Difference in ATAC-seq

1

Hi, everyone. How would I go about quantifying the peak height difference of a particular gene between two a wild type and a mutant in ATAC-seq? A colleague mentioned possibly calculating a moving average of read depths for smoothing and then comparing the peaks after normalization across conditions but said they weren’t sure about what the standard workflow is. What are your thoughts on this? Any help would be much appreciated, as I’m very new to this!


differential


peak


ATAC-seq


calling


analysis

• 90 views

Isn’t that just a differential analysis of the read counts, so the amount of reads intersecting each peak? You can do that with frameworks like edgeR; DESeq2 or limma, or specialized wrappers such as csaw and DiffBind, all in R at Bioconductor.


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