How to interpret track height in Chipseq? 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.
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?