Question: Setting Peak Cutoff Using Minimum # of Reads
gravatar for Andrew Siladi
10 weeks ago by
Andrew Siladi0 wrote:

Is there standard way to set a cutoff for minimum number of reads to consider something an H3K4Me3 peak? The issue we face is that peaks with very few reads often have the greatest fold change in control vs treatment. However, when examining these peaks in IGV sometimes they look real with very few reads in the vicinity, but other times they look like background.

Thank you! Andrew

histone chip-seq h3k4me3 reads • 103 views
ADD COMMENTlink written 10 weeks ago by Andrew Siladi0

That's a usual problem with differential analyses. Along with fold change, use normalized read count (e.g. RPM) as the cut off, e.g. min RPM must be >5.

ADD REPLYlink written 10 weeks ago by venu6.7k
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