====QUMA: QUantification tool for Methylation Analysis====



Developed by Yuichi Kumaki



====QUMA-san: The shell script for sequential QUMA analysis====



Written by Toshiaki Ito

1st November 2019

 

<quma_san_ver2.4.3> 

Systems: Windows Subsystem for Linux (ex. Ubuntu on Windows) 



<quma_san_for_Linux_ver2.4.3> 

Systems: Linux-based OS (ex. Ubuntu 18.04)



========================quma_san_en_ver2.4.3======================== 

This script requires WSL, and QUMA (Character-Based User Interface version) <http://quma.cdb.riken.jp/top/index_j.html> in the system. 

To use WSL, please search yourself.

 To use QUMA (Character-Based User Interface version), please follow instructions in QUMA (Character-Based User Interface version)

You also might need "X11 development files" to execute QUMA (Character-Based User Interface version).



Open the quma_san_en_ver2.4.3, and specify the directory of "quma.pl" in "location" in the line 16 of the script. 

The directory should be like this. ‘/mnt/c/Users/xxxx/..../quma_cui-1.0.0/quma_cui’ 

The following command should be useful to display the directory. 

wslpath -u ‘directory of quma.pl’ (Don’t delete ‘s).





========================quma_san_en_for_Linux_ver2.4.3======================== 

This script requires QUMA (Character-Based User Interface version) <http://quma.cdb.riken.jp/top/index_j.html> in the system. 

To use QUMA (Character-Based User Interface version), please follow instructions in QUMA (Character-Based User Interface version)

You also might need "X11 development files" to execute QUMA (Character-Based User Interface version). 

Open quma_san_en_for_Linux_ver2.4.3, and specify the directory of "quma.pl" in "location" in the line 15 of the script.

The directory should be like this. ‘/mnt/c/Users/xxxx/..../quma_cui-1.0.0/quma_cui’



========================How to use quma_san========================

QUMA-san will create three files as follows.

(1) Overall result of the analysis for each sequence data (textdata_~)

(2) Summary of the analysis for each target region ({Date}_Summary_~)

(3) Methylation pattern diagram ({Date}_dot_~) (open circle: unmethylated CpG, closed circle: methylated CpG)



These three kinds of files can be saved in separate folders.

Analysis can be performed by just answering the questions.

<Tips>

Don't include any hyphens and spaces in names of files and folders.



QUMA-san provides two ways to upload sequence files.

(1) Uploading one by one

(2) Uploading folders which include sequence data. Each folder should include sequence data corresponding to one target genomic sequence.



Read the README of QUMA for options.



========================To start QUMA-san========================



You must change "location" below where quma_san_en_ver.2.4.3.sh or quma_san_en_for_Linux_ver.2.4.3.sh is.



<Windows Subsystem for Linux and Ubuntu on Windows>



Open command prompt



paste next sentence.



wsl bash "location"/quma_san_en_for_Linux_ver.2.4.3.sh 



<Linux OS>



bash "location"/quma_san_en_for_Linux_ver.2.4.3.sh



========================If you need========================



If you need shortcut on windows machine, please follow below.



Open Notepad and paste following two sentences.



wsl bash "location"/quma_san_en_ver.2.4.3.sh

pause



You must change "location" where quma_san_en_ver.2.4.3.sh.



Please save as batch file.