Overview

Unlike regular ChIP-seq data which have a resolution of ~200 bp, MNase digested ChIP-seq produces genomic footprints at single nucleosome level. This gain in resolution allow us to observe tight relations between DNA position and histone marks such as: histone profile at TSS, and alternatively spliced exons.

To harvest this type of data, we have developed nucChIP, a Python package designed to be easy to use by both computational and experimental biologists.

To start analyzing your data with nucChIP follow this installation instructions

As tutorial, we have included detailed application case of nucChIP here

Finally, a summary list of all nucChIP tools are presented here.

To do:
  • Add nucleosome based plots of coverage at 3p and 5p ends of each exon
  • Add control plots of coverage/nucleosome-based on constitutive exons
  • Add other control plots: using publicly available libraries