How to interpret track height in Chipseq?
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?