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negative values in annotatePeaks.pl data Matrix output File

here is my command: annotatePeaks.pl hg19.75.all.tss.srted.bed hg19 -size 6000 -hist 25 -ghist -fpkm -d tag_directory1/ tag_directory2/ > outputfile.txt There are negative values in the second block of the data matrix(the read densities from the 2nd tag directory).I don't understand why the read densities nomalized to fpkm could be a negative value.

chip-seq
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written by daknonzhang • daknonzhang

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