Score column in narrowPeak file?

Hi, I’m trying to carry out a DiffBind operation with peak files (in bed format) generated elsewhere. When selecting my input files and parameters, the default setting for Score Column for a narrowPeak file is column number 8. In my narrowPeak files, column 8 corresponds to the -log10(pvalue). Is this what the score refers to, or should I be changing the column number to correspond to another column, like abs_summit or fold_enrichment? I should note that none of the columns in the narrowPeak file are actually called ‘score’. Thanks in advance!

Hi @alexbisias

Usually, yes, the p-value is what is used for “score” when calculating the FDR.

The file format for narrowPeak datasets is here: Genome Browser FAQ

You’ll notice the first few columns are similar to BED format, which has a score metric in the 5th column, but what that score represents differs between the two plus narrowPeak has two more summary attributes.


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