Decomposition-based peak identification, which find peaks across a large number of TSS (transcription starting site) profiles
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identify_tss_peaks.sh

README.md

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

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