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Question: Extracting Gene Names from BigWig File
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6 months ago by
hamza_karakurt • 10
hamza_karakurt • 10 wrote:

Hello, I have some BigWig files of a ChIP-Seq analysis. I used BigWig compare in Galaxy but I don't know how to find names of differential changed genes.

Is there any tool for this in Galaxy? Or which external tool should I use?

Thank you.
deeptools bigwig chip-seq • 246 views
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modified 6 months ago by Devon Ryan • 1.9k • written 6 months ago by hamza_karakurt • 10
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6 months ago by
Devon Ryan • 1.9k
Germany
Devon Ryan • 1.9k wrote:

You have a couple options. Firstly, diffBind is a standard tool for looking at differential binding. If you don't need p-values, it can be helpful to put your bigWig files into computeMatrix and then plotHeatmap. In plotHeatmap, you can perform k-means clustering to find clusters with more signal in one group vs. another. There's an option to output the regions (and thus the names) in a text file.
ADD COMMENT • link written 6 months ago by Devon Ryan • 1.9k
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