PCA (Principal Component Analysis) plots from ChIP-seq data


I would like to produce PCA (Principal Component Analysis) plots from ChIP-seq data of epigenetic modification (e.g. H3K4me3), under different development stages of the organism that I’m working with (a fungus), and with different strains (genotypes) of it as well.

  • Which tool(s) should I utilize from GALAXY to produce such a plot?

  • What kind of files should I use as an input for my ChIP-seq, in order to produce the PCA plots?

FYI: I have done the whole analysis in GALAXY so far, I used:

Bowtie2: for the mapping and to generate BAM files.
MACS2 for the peak calling for the ChIP-seq.
bamCoverage: to generate bigwig files for visualization.

Any help, would be highly appreciated,

Best wishes,

P.S.: From my search till now, I haven’t found any relevant tutorial for the topic… if, by any chance, you came across such a tutorial, please let me know about it. I`m aware though for the pipeline to produce a PCA from RNA-seq data, but that is not helpful in my case that I have to deal with ChIP-seq data instead…

Hi @Manolis1
Have you seen this post?
Kind regards,

Hi @Igor,

Thank you very much for your prompt response and your suggestion.

I had a look at the DiffBind tool prior to yesterday`s post, but my initial understanding was that it mostly focuses on the differential binding of Protein(or the presence of particular epigenetic marks), to specific regions of the DNA. Hence, I did overlook perhaps one of its functions which is the PCA actually. I am currently working with it, and with my BED (Narrow Peaks) files produced previously by MACS2.

I would like though to include in my PCA more than two groups, and although there is an option of insert group in the DiffBind tool, somehow this is not possible (I click and nothing happens), could you please tell me how can I make this option available?

Greetings & many thanks for your help,


Hi @Manolis1,
Unfortunately, I am not familiar with DiffBind. I could not figure out how to add a new group as well.
Kind regards,