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6.0 years ago
Bioinformatist Newbie
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270
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
