What does the x axis mean for Nucleosome Free Regions (NFR) score plot?

jianhong / ATACseqQC

ATAC-seq Quality Control

https://jianhong.github.io/ATACseqQC/articles/ATACseqQC.html

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What does the x axis mean for Nucleosome Free Regions (NFR) score plot? #46

Closed hyjforesight closed 2 years ago

hyjforesight commented 2 years ago

Hello ATACseqQC, Thanks for developing this amazing package. Could you please tell me what's the meaning of the x axis of Nucleosome Free Regions (NFR) score plot? It says 'the average signals of 400 bp window as X-axis', but the title of NFR score plot shows 'NFRscore for 200bp flanking TSSs'. Thanks! Best, YJ

jianhong commented 2 years ago

Thank you for your good words. The 200bp in the plot title means upstream 200bp + downstream 200bp. Sorry for the confusion.

hyjforesight commented 2 years ago

Hello @jianhong Thanks for the response. Now I get it. Sorry, I'm also confused about the meaning of the values of x-axis. Are they the values of log2 mean coverage, not the distance (bp) to the TSS?

jianhong commented 2 years ago

Yes, they are log2 mean coverage.