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

Question

[Gary]

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. Any suggestion to deal with this kind of 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

Answer 1

[genecats.ucsc]

Hi Gary,

narrowPeak files can be visualized directly on the UCSC Genome Browser as a custom track, no need to convert to bigBed first. However if you wanted to, example 3 on this page: http://genome.ucsc.edu/goldenPath/help/bigBed.html is a good example of how to convert a non-standard bed file to a bigBed file, in that you need to supply bedToBigBed with an autoSql file that describes your data. For more information see this question from our mailing list archive: https://groups.google.com/a/soe.ucsc.edu/d/msg/genome/9PXjH2mlqrE/MrBs3pZ9WLEJ

That being said, I'm slightly confused by the bedToBigBed command you're running, what is FemaleOnly_H3K4me3.bed? Did that come from macs2? According to the macs2 documentation here: https://github.com/taoliu/MACS it appears that this file can be loaded directly onto the Genome Browser. Have you tried that already? I also found this issue: https://github.com/taoliu/MACS/issues/123, which seems to be unresolved, perhaps you could ask there for more information? Lastly, since the number in the score field only determines the darkness of the peak in the genome browser, perhaps you could write a little awk script to check if the values are over 1000 and if so, convert them to 1000.

It would be nice if you could send follow up questions to our mailing list at: https://groups.google.com/a/soe.ucsc.edu/forum/#!forum/genome, this way our entire team will see your question and can help you out, in addition to all the people that follow that list and may not see the question here.

Thanks,

ChrisL from UCSC