Decomposition-based peak identification (DPI)

This tool identifies a set of reference peaks in in genome-wide TSS (transcription starting site) profiles obtained from diverse range of biological states. In particular, this is developed for the FANTOM5 project (Nature 507, 462-467, 2014 and its related papers) that produced CAGE profiles in more than one thousand of biological states in human and mouse, and the analysis results have been available at http://fantom.gsc.riken.jp/5/ as well as the article above.

In general, I recommend to use the FANTOM5 peak set for CAGE analysis, rather than runnning this tool for your own data, so that you can compare your results with others. I would recommend to run this tool to identify a set of TSS peaks in other organisms than human and mouse, or very unique biological conditions not included in the FANTOM5 sample collecttion.

Requirements

• bash (https://www.gnu.org/software/bash/)
• ruby (https://www.ruby-lang.org)
• R (http://cran.r-project.org/)
• R/fastICA package (http://cran.r-project.org/web/packages/fastICA/)
• R/tidyr package (https://cran.r-project.org/web/packages/tidyr/)
• command line tools to operate bigWig files in http://hgdownload.cse.ucsc.edu/admin/
• bedTools (https://code.google.com/p/bedtools/)
• Unix/Linux with Grid Engine (developed with UGE)

Installation

% git clone https://github.com/hkawaji/dpi1.git

How to run

% cd ${INSTALLED_DIR}
% ./identify_tss_peaks.sh [options]

Follow the usage described in the message.

Update (branches)

• beta3 (current master) (Aug, 2018)
  • updated for platform compatibility
• beta2 (June, 2016)
  • updated for compatibility to the recent version of bedtools (v2.25.0) and jksrc (v333).
  • updated for portability of user environment
• beta (Sep, 2014)
  • a wrapper script is updated as 'identify_tss_peaks.sh', enabling to run the steps in any directory.
  • set 'non-decomposition' mode as default
• alpha (April, 2014)
  • a wrapper script '00run.sh' perform all the requried steps.
• core (Dec, 2013):
  • only the core script of R

Author

Hideya Kawaji

Copyright

2014-2017 RIKEN, Japan.

Reference

• A promoter level mammalian expression atlas, Forrest A, Kawaji H, Rehli M, et al. Nature 507, 462-467, 2014