<p>I recently received some .bigwig files from a chipseq experiment.
I loaded the files into IGV.</p>
<p>The interpretation is rather intuitive.</p>
<p>My question is the following:
What exactly do the track heights represent?</p>
<p>For IgG control, the track height is low ranging from 0~5.</p>
<p>For positive controls, such as H3K4me3, I see clear peaks with height ~100.</p>
<p>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?</p>
<p>Thanks so much.</p>

<chip-seq><peak-calling>
How to interpret track height in Chipseq?
# How to interpret track height in Chipseq?

(Asked by: username_0 on 2021-03-17)

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.

**Tags:** chip-seq, peak-calling

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## 0 answers

