Manual

Mac OSX

■ Installation for Mac OSX

  See trouble shooting after the installation.

  Download the installer package and install it on your Mac.

    If your Mac didn't install R and XQuartz, this installer will automatically download these packages and install them.

■ Basic Usage

  Here is sample data

  Preparing input file with samtools

  ・Removing unmapped reads may make the total runtime faster.

  $samtools view -b -F 4 inputfile.bam > inputfile.mapped.bam  #trimming un-mapped reads

  ・Type a following command to sort your bam file. (essential)

  $samtools sort inputfile.bam inputfile

  ・Making index file (essential)

  $samtools index inputfile.bam

  MitoSuite on Mac

  (1) Launch MitoSuite.app

  (2) Load a bam file from Menu bar  |  Ctrl+O

       If menu bar can not be displayed on your Mac, please use “Ctrl+O” command to load a bam file.

       The directory and filename must use only alphanumeric characters.

  (3) Click “Run” button

Linux

■ Automatic installation

  See trouble shooting after the installation.

If you use the automated installer, the installation of MitoSuite is very simple.

Build version  |  Run the automated-installer script (mitosuite_installer.py) in the distribution package.

  $python mitosuite_installer.py

Script version  |  Run the script (MitoSuite_1.0.9b.py) in the distribution package.

  $python MitoSuite_1.0.9b.py

     If you can not install MitoSuite by this script, please manually install following requirement packages.

     After the installation of requirement packages, please run this script again.

■ Manual installation

     Requirement packages for MitoSuite can also be installed manually.

        [1] Install R (with "ggplot2", "reshape2" packages)

        Please install R on your Linux according to r-project.org.

        Open your terminal.app and type a following command to start R console.

     $R

        Then, install "lazyeval","ggplot2" and "reshape2" packages in R console.

        Depending on the version of R, ggplot2's bugs caused by the namespace of lazyeval are reported (https://blog.rstudio.org/2016/11/14/ggplot2-2-2-0/).

        This bug is resolved by installing the latest version of the lazyeval package.

     >install.packages(c("lazyeval",“ggplot2”,"reshape2"),dep=T)

     >q()

        [2] Install Python modules

        You can easily install requirement modules using the following one-line command.

     $sudo pip install numpy scipy pandas 'pysam >=0.8.4,<0.11.0' pyinstaller -U

        Please install PySide based on your Linux system.

        Ubuntu, Debian:

     $sudo apt-get install python-pyside

        CentOS, Fedora, RedHat and RPM-based (as root):

     $sudo yum install python-pyside pyside-tools

        OpenSUSE:

     $sudo zypper ar http://download.opensuse.org/repositories/home:/cgoncalves:/pyside:/ shiboken/openSUSE_11.2/ pyside

     $sudo zypper refresh pyside

     $sudo zypper install python-pyside

        If you can not install PySide by these procedures, please check these pages (https://wiki.qt.io/PySide_Binaries_Linux
        or http://pythoncentral.io/install-pyside-pyqt-on-windows-mac-linux/or http://pyside.readthedocs.io/en/latest/building/linux.html).

■ Basic Usage

Here is sample data

  Preparing input file with samtools

  ・Removing unmapped reads may make the total runtime faster.

  $samtools view -b -F 4 inputfile.bam > inputfile.mapped.bam  #trimming un-mapped reads

  ・Type a following command to sort your bam file. (essential)

  $samtools sort inputfile.bam inputfile

  ・Making index file (essential)

  $samtools index inputfile.bam

  MitoSuite on Linux

  (1) Launch MitoSuite via terminal

  Build version  |  

  $ mitosuite

  Script version  |  

  $ python MitoSuite_1.0.9b.py

  (2) Load a bam file from Menu bar  |  Ctrl+O

       The directory and filename must use only alphanumeric characters.

  (3) Click “Run” button

Optional settings

  - Phred Score threshold

     Threshold value shows the lower of the base-call quality (phred score) to call consensus bases.

  - Pileup method for calling consensus bases

      Majority : Deciding the base by the majority of the number of basecall

         Example 1  |  Total depth at a site = 30 ("A":28, "G":2) → Consensus base : "A"

         Example 2  |  Total depth at a site = 30 ("A":15, "G":15) → Consensus base : "N"

      BestScore : Deciding the base with the highest basecall quality at each site

         Example 1  |  Total depth at a site = 10 ("A":8, "G":2), Best phred score at each bases : "A"(Q=35), "G"(Q=40) → Consensus base : "G"

         Example 2  |  Total depth at a site = 10 ("A":8, "G":2), Best phred score at each bases : "A"(Q=40), "G"(Q=40) → Consensus base : "N"

      Majority + BestScore : Incorporating the best quality method with the majority decision method at each site

         Example 1  |  Total depth at a site = 10 ("A":5, "G":5), Best phred score at each bases : "A"(Q=35), "G"(Q=40) → Consensus base : "G"

         Example 2  |  Total depth at a site = 10 ("A":5, "G":4), Best phred score at each bases : "A"(Q=40), "G"(Q=40) → Consensus base : "A"

Trouble shooting

  [1] Interactive graphs are not drawn on Firefox (ver.67 or later).

    1. Enter "about:config" in the Firefox address bar.

    2. Change the value of “security.fileuri.strict_origin_policy” from true to false.

    Note: This procedure can change the security level of your web browser. After using MitoSuite, please return to the default setting (false to true).

  [2] SVG files are not generated.

    1. Download ggplot2 ver.2.2.1 (less than 3) and install from R.

  $curl -O https://cran.r-project.org/src/contrib/Archive/ggplot2/ggplot2_2.2.1.tar.gz

    or

  $wget https://cran.r-project.org/src/contrib/Archive/ggplot2/ggplot2_2.2.1.tar.gz

  $R CMD INSTALL ggplot2_2.2.1.tar.gz