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Question: Filter Wig file
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gravatar for lukacdm
3.7 years ago by
lukacdm • 0
United States
lukacdm • 0 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?

 

Thanks.

 
wig chip seq • 1.4k views
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modified 3.7 years ago by Jennifer Hillman Jackson ♦ 25k • written 3.7 years ago by lukacdm • 0
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gravatar for Jennifer Hillman Jackson
3.7 years ago by
Jennifer Hillman Jackson ♦ 25k
United States
Jennifer Hillman Jackson ♦ 25k wrote:

Hello,

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 (http://genome.ucsc.edu) 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 COMMENT • link written 3.7 years ago by Jennifer Hillman Jackson ♦ 25k
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