y-axis on IGF viewing .tdf file

Question

[acorella]

Hi,

What does the y-axis in IGV represent when viewing a .tdf file of chIP-seq data generated directly from a .bam file (using IGVTools)?

Is it total reads? Is it normalized?

Thanks!

Answer 1

[dariober]

The y-axis should be the read count averaged in windows (from igvtools docs for count command: -w The window size over which coverage is averaged. Defaults to 25 bp.). The y-axis value can be normalized for library size if the option "Normalize coverage data" is enabled. Note that you have to reload the tracks for this option to have effect.