QDMR:Quantitative Differentially Methylated Region
   
Frequently Asked Questions

 

 

Q1. Is there a command-line version of QDMR?

In order to facilitate the analysis of massive methylation data, a command line version of QDMR is provided now. This version of QDMR can be downloaded from the Download page. No need to install. Download the command line version of QDMR, and unpack the distribution tarball and open up a command terminal. Go to the directory where you unpacked QDMR, and simply run the script as:

java -jar QDMR.jar infile=Example_HEP_Dataset.gct,outfolder=/pub2/liuhb/,SD=0.07

More information can be obtained from tutorial for command line version of QDMR.

Q2. What is the latest version of QDMR?

The latest version of QDMR is 1.0 (Release Note). With the increased functionality, we will develop the later QDMR.

 

Q3. Where can I find the hardware and software prerequisites for QDMR?

The hardware requirements, supported operating systems, and supported browsers is shown in Download site.

 

Q4. How can I get help with QDMR or provide feedback?

The tutorial fully describes QDMR and how to use it. To provide feedback or ask a question send email to hongbo919@gmail.com or yanyou1225@yahoo.com.cn.

 

Q5. How do I install (uninstall) QDMR?

To install QDMR, go to QDMR Download to download the QDMR for your operating system. Then install QDMR by double-clicking or decompressing. To uninstall QDMR, use the utility provided as part of the QDMR installation. If the QDMR uninstall utility is unavailable, delete the QDMR installation folder and remove all QDMR files other than the desktop icons.


Q6. What file format dose QDMR support?

Currently, QDMR with interface only supports Txt file. And the command line version of QDMR supports the gct format only. In the latter version, more file formats will be supported.

 

Q7. Where can I find information about file formats used by QDMR?

Information on file formats supported by the modules currently in QDMR is available in Tutorial.

 

Q8. Is it possible to use plant genomes (especially Arabidopsis thaliana) as reference in QDMR, have you planned to include such a feature?

For your first concern about the application of QDMR in plant species, QDMR is independent of species. Thus, QDMR can be used to analyze plant genomes.

 

Q9. Would it be valid to enter BS-seq data into QDMR and define a "region" of 1 basepair in order to treat a single position as a DMR?

QDMR can be used for both single nucleotide positions and genomic regions. But, if your input data are single positions, we think the result of QDMR should be differentially methylation nucleotide sites (DMS).

 

Q10. I hit the "import" button, QDMR showed 10% done, then it just stopped there. what is wrong?

There are some reasons for this problem. Some operation guides have been imbedded in the import interface.What's more, it is recommended the example data are viewed before you set your own data format. The example data can be found in the attachment. If you still cann't resolve your problem, we would like to help you check your data if you can send some data to us.

 

Q11. I am wondering may I have source code of QDMR ?

We would like to share the source code of QDMR with you. The source code can be modified as you need only in scientific research. Any commercial use is prohibited. Moreover, QDMR source code-based software development is also prohibited due to software copyrights(Copyright Protection Center of China,2011R11S006683). Any changes to the source code should be listed when you publish papers using the modified version.Click here to download the source code of QDMR verson 1.0 which is can be opened and edited in Eclipse higher than 7.5.

 

Q12. I'm trying the QDMR software with your example dataset and the default parameters. I downloaded and installed the standalone software without any trouble, but when I try to indetify the DMRs the proccess get stuck at 5% (it has been running for 6 hours so far). Could you tell me, how much use to spend the proccess for the first example dataset?

Thanks for your interest in our approach QDMR.I am so sorry for the inconvenient given to you.Under normal circumstances, it takes about two minutes for the first example dataset. I tried the QDMR software with your example dataset and the default parameters on my computer again, and it can work glibly. All tasks for the first example dataset took less than two minutes matter-of-factly. I have two suggestions for you. First, try QDMR on another computer again. Second, try the online version of QDMR at its website http://bioinfo.hrbmu.edu.cn/qdmr/ by clicking “LAUNCH NOW!”.I am also very sorry to tell you that we didn't develop a command line version of QDMR. The java version of QDMR can be used to analyze the methylation files in most cases. Best wishes to you! Please contact us for any further questions about QDMR.


Q13.Other
If you have any trouble or recommendations, please send an email to yanyou1225@yahoo.com.cn or hongbo919@gmail.com

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