Chip-Seq and DeepTools

Question

[qudrat.nii]

Hello,

I have Chip-Seq data for two transcription factor (TF1,TF2) and they have significant numbers of peaks overlapped (MACS2 Peak calling) and I want to plot linear correlation between the signal of TF1 and TF2 peaks in the shared binding sites. Please guide me. Thank you

[Ram]

Please use more descriptive titles. Also, don't repeat your titles across multiple questions. Plus, don't copy paste your title in the tags field.

Answer 1

[bk11]

You can do something like this for your shared binding site in R.

library(ggplot2)

#Creating data for your TF signals
TF1_S <- c(3.2, 4.5, 5.6, 2.1, 6.7)
TF2_S <- c(2.8, 3.9, 5.0, 1.8, 6.2)

#Create dataframe
data <- data.frame(TF1 = TF1_S, TF2 = TF2_S)

#Calculate Correlation using `cor()` function
correlation_coefficient <- cor(data$TF1, data$TF2)

#Plot correlation Scaterplot in ggplot2
ggplot(data, aes(x = TF1, y = TF2)) +  geom_point() +
           labs(title = "Linear Correlation between TF1 and TF2 Peaks",
           x = "TF1 Signal", y = "TF2 Signal") +
          geom_smooth(method = "lm", se = FALSE, color = "red") +
         geom_text(x = min(data$TF1), y = max(data$TF2), label = paste("Correlation:", round(correlation_coefficient, 2)))

[qudrat.nii]

Where do you get TF signals from? I have bigwig file for TFs. How to get signal from these files?

[bk11]

I made mock signals for illustration purpose. Please check the link below for how to get signals from your bigwig files-

How to extract bigWig signal for a given bed file?

Getting peak heights from TF chIP-seq data (wig file)