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I recently received some .bigwig files from a chipseq experiment. I loaded the files into IGV.

The interpretation is rather intuitive.

My question is the following: What exactly do the track heights represent?

For IgG control, the track height is low ranging from 0~5.

For positive controls, such as H3K4me3, I see clear peaks with height ~100.

Do track heights simply mean the number of reads mapped to that genomic interval during peak calling? Does it literally mean there are ~100 reads that aligned to that region in the H3K4me3 .bam file?

Thanks so much.

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Depends how the files were made. In the simplest case yes, the height represents the pipeup of reads from the BAM file that was used. For a direct (visual) comparison you have to normalize the files though as otherwise sequencing depth confounds the height of the peaks, like if file A has ten times more reads and the peak is 10 times higher than in B then this is probably only due to differences in total read number (=sequencing depth). I wrote down my preferred method to do that in this biostars post: https://www.biostars.org/p/413626/#414440

Does this make sense to you?

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