modENCODE Galaxy on Amazon Cloud
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README.md

modENCODE-DCC: Galaxy

This GitHub repository contains tools and scripts put together by members of the modENCODE DCC team:

  • Quang Trinh
  • Marc Perry
  • Sergio Contrino
  • Lincoln Stein

Alumini:

  • Ellen Kephart
  • Ravpreet Setia
  • Fei-Yang ( Arthur ) Jen
  • Ziru Zhou
  • KarMing Chu

We would like to thank Bjoern Gruening (bjoern.gruening@gmail.com) for updating many of our scripts to take advantages of the newer Tool Shed features. Please send your comments/questions to modENCODE DCC at help@modencode.org.

Documentations

README file on how to launch an instance of Galaxy on Amazon Cloud.

README file on how to use the ENCODE/modENCODE uniform processing/peak calling pipeline ( macs2, IDR, and IDR-plot ) in Galaxy on Amazon Cloud.

README file on how to use the ENCODE/modENCODE uniform processing/peak calling workflows ( macs2, IDR, and IDR-plot ) in Galaxy on Amazon Cloud.

README files on how to use Amazon Cloud AMI or Bionimbus Cloud to run the uniform processing/peak calling pipeline from the command line

Galaxy Tools

The tools listed below are also on Galaxy Toolshed

modENCODE_DCC_tools/bamedit - merging, splitting, filtering, and QC of BAM files

modENCODE_DCC_tools/idr - Reproducibility and automatic thresholding of ChIP-seq data, written by Anshul Kundaje ( https://sites.google.com/site/anshulkundaje/projects/idr )

  • mac2npk - converts macs output peak file to ENCODE narrowPeak format
  • idr - consistency analysis of peak files
  • idr-plot - plot consistency analysis on IDR output files
  • IDR Google discussion group - https://groups.google.com/group/idr-discuss

modENCODE_DCC_tools/macs - model-based analysis of ChIP-Seq (1.4.1), written by Tao Liu

modENCODE_DCC_tools/macs2 - model-based analysis of ChIP-Seq (2.0.10.2), written by Tao Liu ( https://github.com/taoliu/MACS )

modENCODE_DCC_tools/peakranger - multi-purpose, ultrafast ChIP-Seq peak caller, written by Xin Feng ( http://ranger.sourceforge.net/ )

modENCODE_DCC_tools/spp - cross-correlation analysis package ( http://code.google.com/p/phantompeakqualtools/ )

Reference

Getting Started with Galaxy CloudMan