Hello, I got some trouble with the output file from Homer's findPeaks, and I hope to get wisdom from you guys.
I performed findPeaks with tag directories from an IP bam file and an input bam file.
I added some options because the library was strand-specific and paired-end.
The command I entered is like this:
findPeaks [IP tag directory] -i [INPUT tag directory] -strand separate -region -size 150 -minDist 370 > output.txt
Then I got an output file like this:
.
I understand the 'Control' means input data,
and I know that p-value cutoff against control data is set to be 0.0001 by default (written in findPeaks manual - 'Filtering Peaks').
But, can you see column 12 (p-value vs Control) ?
Many numbers in p-value column are over 1.
So I thought 'Aha this is a form of transformed value such as log'.
But maybe it's not, because the minimum value was 0.5 .
As I know, p-value cutoff was automatically set as 0.0001, and the number 0.5 couldn't be reasonably produced by log transformation.
Please give me some advice about what the numbers are...
