I am using MACS2 to call open chromatin regions in a MNase-seq dataset. However I'm generating negative p-values after calling broad peaks using the following commands:
macs2 callpeak -t treatment.s.bam -c input.bam -n tg \
--outdir ~/nucleosomedata/ -f BAMPE -g 1.87e9 --broad
Here is a few rows of output:
chr start end length pileup -LOG10(pvalue) fold_enrichment -LOG10(qvalue) name
chr1 3003373 3003936 564 -1.23335E+31 -1.26269E+18 1.36546E+30 2.13806 tg_peak_1
chr1 3020520 3020966 447 -4.20326E+31 -4.30325E+18 4.65349E+30 1.28417 tg_peak_2
chr1 3029027 3030664 1638 -1.39736E+31 -1.4306E+18 1.54704E+30 1.49317 tg_peak_3
chr1 3045122 3045422 301 -5.30715E+31 -5.4334E+18 5.87561E+30 1.26046 tg_peak_4
Could this be due to defaulting to q-values when calling broad peaks?
Thanks
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