PeakXus: comprehensive transcription factor binding site discovery from ChIP-Nexus and ChIP-Exo experiments

We describe a peak caller PeakXus that is specifically designed to leverage the increased resolution of ChIP-exo/Nexus and developed with the aim of making as few assumptions of the data as possible to allow discoveries of novel binding patterns. We apply PeakXus to ChIP-Nexus and ChIP-exo experiments performed both in Homo sapiens and in Drosophila melanogaster cell lines. We show that PeakXus consistently finds more peaks overlapping with a TF-specific recognition sequence than published methods. As an application example we demonstrate how PeakXus can be coupled with unique molecular identifiers (UMIs) to measure the effect of a SNP overlapping with a TF binding site on the in vivo binding of the TF.
Availability and Implementation: Source code of PeakXus is available at https://github.com/hartonen/PeakXus
Contact: [e-mail] or [e-mail]

Source: Bioinformatics - August 31, 2016 Category: Bioinformatics Authors: Hartonen, T., Sahu, B., Dave, K., Kivioja, T., Taipale, J. Tags: GENES Source Type: research