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I am using MACS2 on ChIP-seq data. In the resulting <name>_peaks.xls file, I had understood the "pileup" column to be something like the fragment height of that peak at its summit. Is that correct?
In the last several runs, on many different data sets, I've gotten large negative values for pileup, such as -5.88234959330369E+35. All of the peaks have negative values, and this is true when I run it against the IgG control or no control. Any ideas what this means?
Here is my call to macs:
In the last several runs, on many different data sets, I've gotten large negative values for pileup, such as -5.88234959330369E+35. All of the peaks have negative values, and this is true when I run it against the IgG control or no control. Any ideas what this means?
Here is my call to macs:
Code:
macs2 callpeak --treament <bamfile> --name <name> --gsize mm --format BAM --qvalue 1e-05 --broad