Cut&Run and heatmap

Question

[qudrat.nii]

Hello guys, I am doing cut&run analysis for some transcription factors and I have three replicates of BAM files and three replicates of MACS2 output. For downstream studies should I merge three replicates of bam file to plot heatmap? In case replicates are not highly correlated what should I do?

[ATpoint]

Do not delete questions that received answers, it's plain disrespectful towards the users who ivnested time into your question. After all, biostars is a knowledge repository so the Q/A might serve others in the future. It's all anonymous here if you set your account accordingly, so don't worry about the irrational fear of people pointing fingers at you, it's not a realistic issue.

Answer 1

[rpolicastro]

deepTools is great for general plot making for CUT&RUN, ChIP-seq, and the like. If you have any other plots you want to make in mind you should include an example so we can give more specific advice.