Question: Roadmap epigenomics narrowPeak and broadPeak contain scores > 1000
gravatar for F Lekschas
18 months ago by
F Lekschas10
Cambridge, MA
F Lekschas10 wrote:

How should the score of consolidated narrowPeak and broadPeak Roadmap Epigenomics files be interpreted? The bed format dictates that the score has to be between 0 and 1000 and according to the Roadmap Epigenomics the format for their narrowPeak and broadPeak files follows UCSC standards. Unfortunately, it seems like this is not always the case.

For example, the first few lines of E003-H3K4me3.narrowPeak.gz look like:

chr16 20751573  20753603  Rank_1 3574 . 84.81562 357.44171 348.55319 1415
chr2  85764275  85768872  Rank_2 3548 . 71.33364 354.87430 346.61420 2158
chr1  110879746 110884121 Rank_3 3486 . 80.68906 348.62274 340.97101 2449

The score in column 5 is higher than 1000.

Am I misunderstanding/missing something or is this an issue with peak calls from the Roadmap Epigenomics project? Does someone know how to easily convert this into a valid BED6+4 format?

epigenomics chip-seq • 539 views
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