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Shintaro Katayama edited this page Apr 16, 2015 · 48 revisions

STRTprep (https://github.com/shka/STRTprep) is an open-source software package for analysis of STRT RNA-seq data. The version 2 contains preprocessing step of the sequenced raw reads, alignments, quantitation, quality check, and moreover statistical test of the differential expression. The version 3 contains TFE-based quantification. This package can run on both Linux and OSX.

Installation of prerequisite softwares

This instruction is for the v3dev

For installation of the basal softwares to prepare your (copy of) STRTprep, check the following requirements; but you do not need to install Homebrew or Linuxbrew themselves into your system.

xcode-select --install on your Terminal.app, for easy install of Command Line Tools.

DO NOT UPGRADE/INSTALL the Command Line Tools for Xcode version 6.3, released in April 8th! (why?) Solution is downgrade to the version 6.2 - you can get the old version from Xcode at Apple developer center.

Moreover, you might need more packages as follows.

  • mysql-devel (for kent-tools on CentOS)
  • imake (for openssl on CentOS)
  • python-setuptools (for cmake on CentOS)

Preparation of STRTprep folder for your project

STRTprep consists one folder containing configurations and scripts. One STRTprep folder is for one project. You can give any name for the project folder, but here we use STRTprep3.test for example.

git clone -b v3dev https://github.com/shka/STRTprep.git STRTprep3.test
cd STRTprep3.test

There is a script for installation of the additionally required softwares. You need to run it only once when you create the project folder.

bin/install.sh

After the installation, you need to load configuration written in bin/setup.sh into your shell environment, everytime when you would like to proceed tasks within the project folder.

Preparation of bowtie indexes

You need to prepare three indexes for (i) phyX, (ii) genome+spike-in, and (iii) transcriptome. There are scripts to build the indexes.

  1. PhyX index
  • bin/index_phyX.sh; create at src/ebwt/phyX/ref
  1. Genome+spike-in index
  • bin/index_hg19_ercc92_ynbA_u13369.sh; create at src/ebwt/hg19_ercc92_ynbA_u13369/ref
  • bin/index_mm9_ercc92_ynbA_bk000964.sh; create at src/ebwt/mm9_ercc92_ynbA_bk000964/ref
  • bin/index_canFam3_ercc92_ynbA.sh; create at src/ebwt/canFam3_ercc92_ynbA/ref
  • bin/index_susScr3_ercc92_ynbA.sh; create at src/ebwt/susScr3_ercc92_ynbA/ref
  1. Transcriptome index; requires two options - (i) genome version, and (ii) genome+spike-in index
  • bin/index_ensGene.sh; create based on ENSEMBL at src/ebwt/ver_ensGene/ref
  • bin/index_knownGene.sh; create based on UCSC known genes at src/ebwt/ver_knownGene/ref
  • bin/index_refGene.sh; create based on RefSeq at src/ebwt/ver_refGene/ref

The following is an example to build the indexes on hg19 and RefSeq; the RefSeq transcritome index is at src/ebwt/hg19_refGene.ref.

. bin/setup.sh
bin/index_phyX.sh
bin/index_hg19_ercc92_ynbA_u13369.sh
bin/index_refGene.sh hg19 src/ebwt/hg19_ercc92_ynbA_u13369/ref

Tips

  • Do not contain space (or special character, which you need escape) in the pathname of (sequence-/index-/etc-)files and your project folder.
  • Microsoft Office 2011 (for mac) uses ";" (semicolon) instead of "," as column separater, when you use OSX with Europian regions. Please change the primary "Language" at System Preferences to, for example, US, if you would like to edit the CSV (comma-separated-values) files for the pipeline.

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