y-axis on IGF viewing .tdf file
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!
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dariober
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acorella •
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acorella •
1 answer
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.
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