Visualizing a set of genes in ENCODE ChIPseq dataset-Any tools or tutorials?
Hi, I have a few set of genes (about 100-200) which I want to show that are enriched for binding with some transcription factors using ENCODE ChIPseq data. So I can get narrowpeak or bigwig files from ENCODE, however, I want to focus on only the genes in my list (mentioned above) and visualize something similar to CHIPSEEKER visualization (similar to abstract heatmap). If anyone know how to feed the data in Chipseeker (R) or suggest any other tools that can do it, would really help. Thanks. Best regards, Jinesh
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You can try
deepToolsExample usage with bigwig files: https://deeptools.readthedocs.io/en/develop/content/tools/plotHeatmap.html#usage-examples
You can plot only the regions corresponding to your genes-of-interest by creating a
.bedfile and supplying it to deepTools'scomputeMatrixcommand.Thank you. I will look into this. Seems like a viable option.!!