Hello guys,

from your experience with chip-seq analysis what would be the most useful visual representations of chip-seq results?
I am particularly interested in your opinion on visualizations of motif discovery, annotation and differential binding analysis and your experiences with various bioinformatics tools that you' ve been using for this purpose.

Cheers,
Nemanja

If you have a lot of samples (including replicates), it can be very useful to visualize sample clustering. Examples include heatmaps with hierarchical clustering and PCA. The [DiffBind package in Bioconductor][1] provides clustering and PCA plots, as well as MA, box, and volcano plots after performing the differential analysis. You can then feed the differential sites into some of the excellent tools above.



  [1]: https://bioconductor.org/packages/release/bioc/html/DiffBind.html