Chip-seq biological replicates, multiple timepoints


So unfortunatelly our bioinfo guy is unavailable and I need to analyze my ChIP-seq data myself. I need some guidance for the analysis with multiple biological repeats and differential binding between the treatments.

I am checking histone marks distribution in the rat tissue at different age. I have 10 biological repeats/ per timepoint, and 4 different timepoints. What I would like to get is a list of genes marked by given histone mark at each timepoint (relatively easy), but then also observe the change of the binding of histone marks at different timepoints, so do some differential analysis.

What should I do? Merge the BAM files at this stage (quite problematic, since the files are big and using quite a lot of space) and call the peaks on the merged file? How to compare then the difference in binding between the timepoints?

Should I rather call the peaks separately for each biological repeat and then merge the BED files together at the level of MACS2? Then once again, how to compare the difference between the timepoints.

Is there any step by step tutorial? I have seen there are some tools like diffbind or multiGPS, I am reading the papers describing them, but honestly I am quite lost (or stupid) and need some easier description of the process.

Hello @dkomar

Hopefully you have found the tutorials already, but if not please find them here. The site can be searched with keywords like datatypes and tool names, or navigated by analysis domain.

Many tools will also have a help section with examples plus link-outs for citations/publications and author resources.