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I am using deepTools to create heatmaps from .bw files created when running CUT-RUNTools-2.0. I am interested in the Y-axis of the heatmap which is plotted in the units of the bigWig file used to create the matrix and subsequent heatmap. So, to understand the Y-axis of the heatmap, I need to understand the units of the bigWig file.
The .bw file I am using is specifically the .cpm.norm.bw file in the peakcalling/macs2.narrow folder.
I am assuming that the units would be counts (reads) per million for each 120 base fragment. I am not exactly sure about the fragment size. I am using defaults in my bulk-config.json file. I would also like to understand how the normalization works. It seems to me cpm would be a normalization. Is there any other normalization other than counts per million ?
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I am using deepTools to create heatmaps from .bw files created when running CUT-RUNTools-2.0. I am interested in the Y-axis of the heatmap which is plotted in the units of the bigWig file used to create the matrix and subsequent heatmap. So, to understand the Y-axis of the heatmap, I need to understand the units of the bigWig file.
The .bw file I am using is specifically the .cpm.norm.bw file in the peakcalling/macs2.narrow folder.
I am assuming that the units would be counts (reads) per million for each 120 base fragment. I am not exactly sure about the fragment size. I am using defaults in my bulk-config.json file. I would also like to understand how the normalization works. It seems to me cpm would be a normalization. Is there any other normalization other than counts per million ?
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