Question: what do negative values from bigWigAverageOverBed output mean?
gravatar for Apoorva
4.5 years ago by
United States
Apoorva270 wrote:


This might seem basic, but I have a bed file with promoter regions I am interested in and Bigwig files from my ChIP-Seq experiment after subtracting input from treatment files using deeptools bamcompare. I want to know the coverage of my bw files. I came across the bigWigAverageOverBed utility from UCSC that I used but I am not sure I understand the results. Can anyone help me understand how this utility works and what negative values of the score mean?


ADD COMMENTlink modified 4.5 years ago by Devon Ryan98k • written 4.5 years ago by Apoorva270
gravatar for Devon Ryan
4.5 years ago by
Devon Ryan98k
Freiburg, Germany
Devon Ryan98k wrote:

If the normalized input level is, on average, higher than that of the ChIP (at least in the regions of interest) then the average value will be negative.

ADD COMMENTlink written 4.5 years ago by Devon Ryan98k

Thank you Devon. I have data that looks like this

chr chr_start chr_end ENSEMBL Diff_cell undiff_cell

chr2 76542036 76825604 ENSMUSG00000051747 -3.09314 7.20316

-3.093 and 7.2 are average coverage values of the differentiated cell sample and undifferentiated cell sample. Now i need to know if this gene and other genes with similar values are enriched in any GO category. Would it be right to log transform the average coverage (form bigWigAverageOverBed), calculate the fold change and use the FC to create a ranked list of genes for GSEA ? In that case, how do i log transform large negative values ?

ADD REPLYlink modified 4.5 years ago • written 4.5 years ago by Apoorva270

The only way for fold-changes to make sense is if you put a floor of 0 on the values and add a small value to everything.

ADD REPLYlink written 4.5 years ago by Devon Ryan98k
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