Requirement

» Hardware: 32-bit or 64-bit computer running Linux (5 Centos or later); 16 GB of RAM

» PHP 5.3.15 or later (How To Update) and modify php.ini (at least 8G RAM in variable memory_limit)

        vim /etc/php.ini
        memory_limit = 8096M

» Apache

» Web server environment(/var/www/html or /home/user/public_html); miRTarCLIP needs to execute in x86 or x64 bit Linux systems. And the web broser page needs a web server environment. Generally, the web pages can be created in Linux /var/www/html or /home/user/public_html directory. Before download miRTarCLIP, you should test your system can perform a web server (type: "your server ip/~user/" in browser, if this address is work, you can download the miRTarCLIP and start to analysis).

Quick Start and Install

» Set up a web server environment in /var/www/html or /home/user/public_html:

» Download miRTarCLIP source code to the directory /var/www/html or /home/user/public_html:
   Linux x32:miRTarCLIP_x32
   Linux x64:miRTarCLIP_x64

        cd /home/user/public_html or cd /var/www/html
        wget http://mirtarclip.mbc.nctu.edu.tw/download/miRTarCLIP_x64.tgz

» Uncompress miRTarCLIP source code:

        tar -zxvf miRTarCLIP_x64.tgz

» Change into miRTarCLIP directory

        cd miRTarCLIP_x64

» See your local directory by pwd, copy your local directory

        pwd

» Modify setting.php variable: $MIRTARCLIP_PATH=

        vim setting.php (modify $MIRTARCLIP_PATH to "/home/user/public_html/miRTarCLIP_x64")
        chmod 777 -R public_html/results

» You can run example case to initialize the system, download TargetScan files, and test your system.

        php run_parclip_human_example.php

» If any error happen, you can check the TargetScan files at ref/targetscan/9606 in hunam or ref/targetscan/10090 in mouse. The directory should contain at least these five files, Conserved_Family_Info.txt, Conserved_Site_Context_Scores.txt, Nonconserved_Family_Info.txt, Nonconserved_Site_Context_Scores.txt, and UTR_Sequences.txt. If any files are not involved in this directory, you can download these files from TargetScan.
Human: http://www.targetscan.org/cgi-bin/targetscan/data_download.cgi?db=vert_61
Mouse: http://www.targetscan.org/cgi-bin/targetscan/data_download.cgi?db=mmu_61

» Now, you can open your browser and type your web site to see the analysis results:

        In browser: your ip/~user/miRTarCLIP_x64/public_html/

Case study for one dataset

» If you success in our example analysis, now you can analysis your own dataset.
» We use Hafner et al., 2010 Cell, AGO1(SRR048973) as an example.
» You should download raw data (.sra, .fastq, or .fa) in "input" dictionary

        cd input
        wget http://tinyurl.com/9yss5t5
        cd ..

» Create a new program for PAR-CLIP analysis.
» If you want to analysis CLIP-Seq, please copy run_clip_mouse_example.php

        cp run_parclip_human_example.php run_SRR048973.php

» Create a new task for run_SRR048973.php

        cp tasks/task_setting.parclip_human_example.php tasks/task_setting.SRR048973.php

» Editing task file for your raw data.

        vim tasks/task_setting.SRR048973.php

» All of the annotation mark in the program.
» Here, only modify two parameter $TASK_NAME and $FILE_FORMAT.
» task_setting.SRR048973.php => $TASK_NAME = "SRR048973"

        $TASK_NAME = "SRR048973";

» Raw data file format are .sra.

        $FILE_FORMAT="sra";

» Editing run_SRR048973.php

        vim run_SRR048973.php
        $TASK_FILES = Array(
                'tasks/task_setting.SRR048973.php'
        );

» Start to run this case (SRR048973).

        php run_SRR048973.php

» You can open your browser and type your web site to see the analysis results.

Case study for multiple dataset

» We use Hafner et al., 2010 Cell, SRR048974, SRR048975, and SRR048976 as an example.
» You should download these three raw data to "input" dictionary.
» Create a new program for Multiple PAR-CLIP analysis.

        cp run_parclip_human_example.php run_Multiple_parclip.php

» Create three new task for run_Multiple_parclip.php

        cp tasks/task_setting.parclip_human_example.php tasks/task_setting.SRR048974.php
        cp tasks/task_setting.parclip_human_example.php tasks/task_setting.SRR048975.php
        cp tasks/task_setting.parclip_human_example.php tasks/task_setting.SRR048976.php

» Editing task file for your raw data like previous step: editing $TASK_NAME and $FILE_FORMAT.

        vim tasks/task_setting.SRR048974.php
        $TASK_NAME = "SRR048974";

        vim tasks/task_setting.SRR048975.php
        $TASK_NAME = "SRR048975";
        $FILE_FORMAT="sra";

        vim tasks/task_setting.SRR048976.php
        $TASK_NAME = "SRR048976";
        $FILE_FORMAT="sra";

» Editing run_Multiple_parclip.php

        vim run_Multiple_parclip.php
        $TASK_FILES = Array(
                'tasks/task_setting.SRR048974.php'
                'tasks/task_setting.SRR048975.php'
                'tasks/task_setting.SRR048976.php'
        );

» Start to run this case.

        php run_Multiple_parclip.php

» You can open your browser and type your web site to see the analysis results.

Current Version

  • » Release 1.0.1 at 2013.11.30

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