Question about different lengths of fragments in ATAC-seq
Hi all,
Would you please explain why longer fragments don't always mean more open chromatin regions? That we need to re-center the peak. I still haven't understood this step. As I understand, transposase will cut more open regions of varying in lengths, and less open regions will create shorter lengths. So on average, cells with more open regions will have longer fragments than cells that are less open. Thank you so much!
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Where are you getting this from? (when you mention that thing that everyone is supposed to know, it helps to give it some context, or reference it directly.)
I try to understand why we need re-center the peak. That is my understanding after reading the explanation from ChatGPT 😅.