Question: How to plot the TF binding occupancy around a specific regulatory region?
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gravatar for Bioinformatist Newbie
2.2 years ago by
Germany
Bioinformatist Newbie250 wrote:

I have an enhancer region of NANOG (chr12:6831533-6857455) and potential TF binding sites for some other TFs (SOX2, POU5F1, KLF4 and NANOG) in this enhancer region. I want to plot the location and distribution of peaks in this enhancer region, and ChIPseeker seems a reasonable option for me. However, I am unable to understand how I can modify it for my purpose, as ChIPseeker takes as input the annotated peak files for different TFs while what I have here is only the binding coordinates and the reference coordinates, across which I want to see which TF is binding where (e.g. which TFs are usually closer and which are further apart). Below is how my data looks like, any help will be much appreciated!

chr12   6851911 6852155 SOX2    244     chr12   6831533 6857455 1.86    GH12G006940     11      NANOG   10.68
chr12   6851918 6852135 NANOG   217     chr12   6831533 6857455 1.86    GH12G006940     11      NANOG   10.68
chr12   6851947 6852212 SOX2    265     chr12   6831533 6857455 1.86    GH12G006940     11      NANOG   10.68
chr12   6852034 6852866 SOX2    832     chr12   6831533 6857455 1.86    GH12G006940     11      NANOG   10.68
chr12   6852195 6852552 KLF4    357     chr12   6831533 6857455 1.86    GH12G006940     11      NANOG   10.68
chr12   6852270 6852667 POU5F1  397     chr12   6831533 6857455 1.86    GH12G006940     11      NANOG   10.68
chr12   6852291 6852522 POU5F1  231     chr12   6831533 6857455 1.86    GH12G006940     11      NANOG   10.68
chr12   6852312 6852584 POU5F1  272     chr12   6831533 6857455 1.86    GH12G006940     11      NANOG   10.68
chr12   6852313 6852588 SOX2    275     chr12   6831533 6857455 1.86    GH12G006940     11      NANOG   10.68
chr12   6852350 6852639 NANOG   289     chr12   6831533 6857455 1.86    GH12G006940     11      NANOG   10.68
chr12   6852354 6852619 POU5F1  265     chr12   6831533 6857455 1.86    GH12G006940     11      NANOG   10.68
chr12   6852357 6852668 SOX2    311     chr12   6831533 6857455 1.86    GH12G006940     11      NANOG   10.68
plot tf-binding chip-seq • 559 views
ADD COMMENTlink modified 2.2 years ago • written 2.2 years ago by Bioinformatist Newbie250
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