How to make the Input track flat for ChIP-seq

Question

[dharitrisaikia162]

Hello everyone

We were analyzing our ChIP seq data of our protein on human rDNA (ribosomal DNA ) locus, after mapping it with hg-38 human genome assembly modified for rDNA analysis (https://doi.org/10.1016/j.jbc.2023.104766). we generated .BW files through BamCoverage for both input and IP, then we used MACS2 to find the significant peaks with q -value 0.001, and we got significant binding on rDNA locus. However, we want to make the input track flat with respect to the IP and to retain the significant peaks in the IP track only. Kindly help us regarding this. We have attached the IGV snap shot of our input and IP replicates. Tracks are shown in replicates, also the narrowpeak files from MACS2 are shown

Answer 1

[Trivas]

I'm a big fan of the Homer suite of tools for ChIP-seq analysis, maybe this will help: http://homer.ucsd.edu/homer/ngs/mergePeaks.html

[dharitrisaikia162]

Thanks. We'll try this and update you soon.

Answer 2

[Ian]

If the intention is to subtract input from IP you could try bigwigCompare from Deeptools.