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Demultiplexer for Quartz-Seq2

Requirements

system

  • docker
  • docker wrapper for Open Grid Scheduler

software

  • samtools 1.3 (fs000:5000/itoshi/samtools)
  • Picard (fs000:5000/danno/picard:1.0)
  • R + DNABarcodes (fs000:5000/danno/pyper:1.2)
  • Ruby (fs000:5000/itoshi/ruby:2.5.1)

setup

$ cp -a /data2/itoshi/demultiplexer .
$ cd demultiplexer

Edit config.yaml. Please add fastq directory and barcode file path to config.yaml. You should change User ID and Group ID in docker command (-u option).

Usage

$ rake correct_barcode
$ rake correct_bam
$ rake demulti

Setup rbenv

mkdir ~/src
cd ~/src
git clone https://github.com/rbenv/rbenv.git ~/.rbenv
echo 'export PATH="$HOME/.rbenv/bin:$PATH"' >> ~/.zshrc
~/.rbenv/bin/rbenv init

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Demultiplexer for Quartz-Seq2

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