The scores of 5th column (integer score for display) in macs2 NAME_peaks.narrowPeak file are larger than 1000

[Yung-Chih Lai]

Hi,

I have asked this question on Biostars, but nobody answered me.

I use macs2 for peak calling, and obtain a NAME_peaks.narrowPeak file. Its 5th column (integer score for display) is for display purpose on UCSC Genome Browser. However, I find that some scores are larger than 1000 when I convert bed to bigbed using bedToBigBed as the below. Please check my bed file in the attached. Any suggestion to deal with this error? Many thanks.

gary > bedToBigBed -type=bed6+4 FemaleOnly_H3K4me3.bed galGal4.chrom.sizes FemaleOnly_H3K4me3.bigbed

pass1 - making usageList (445 chroms): 3 millis

Error line 1358 of FemaleOnly_H3K4me3.bed: score (1137) must be between 0 and 1000

Best,

Gary