Question: Filter Wig file
gravatar for lukacdm
3.7 years ago by
United States
lukacdm0 wrote:

I would like to filter a wig file from a ChIPSeq Peak calling program by its control ChIPSeq Peak wig file, i.e., to output only peaks that have greater height in the ChIP antibody from the control antibody, or from the input file.  I would like the output to be wig or bigwig for IGV visulatization.  Does anyone know of a method by which I can do this? is there a Galaxy app that will do this?




wig chip seq • 1.4k views
ADD COMMENTlink modified 3.7 years ago by Jennifer Hillman Jackson25k • written 3.7 years ago by lukacdm0
gravatar for Jennifer Hillman Jackson
3.7 years ago by
United States
Jennifer Hillman Jackson25k wrote:


MACS performs peak calling using both tag and control datasets. Some of the output choices are wig data (that can be converted to bigWig). SICER is another choice. These is probably the most straightforward way to do the operation.

There are no tools that I am aware of that will compare two wiggle files directly in a way that permits one to be "subtracted" from the other based on regional coverage. That said, you can check the UCSC tool kit ( to see what is available. Another option is to convert the data to bed/interval format and then compare using tools in the "BEDTools" or "Operate on Genomic Intervals" tool groups.

Best, Jen, Galaxy team

ADD COMMENTlink written 3.7 years ago by Jennifer Hillman Jackson25k
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