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ARSDA (Analyzing RNA-Seq Data)

Name:ARSDA (needs 32 GB of RAM*)
Keywords:RNA-seq, transcriptomics, bioinformatics, next-generation sequencing (NGS), high-throughput sequencing (HTS), Illumina
Version:1.1.0.0
Publisher:XiaLab
Manual:Quick-Start Guide
Support:I respond to and act upon email queries right away
Citation:Xia X (2017) ARSDA: A New Approach for Storing, Transmitting and Analyzing Transcriptomic Data. G3: Genes|Genomes|Genetics

* needed only for four menu items under 'File': 'FASTQ to FASTQ+', 'FASTQ to FASTA+', 'FASTA to FASTA+', and 'Paired FASTAQ files to Paired FASTA+ or FASTAQ+ files'. The functions will finish in minutes with 32 GB of memory, but may take hours or even days with less memory.

I assume that the ',' is comma and '.' is decimal point. This may cause problems in places where ',' is the decimal point. Some functions in ARSDA involve writing text out to a file and then read it back. A string such as "A,B,0.2,0.3" is interpreted to have four columns with ',' as column separator. In "decimal-comma" countries, the same text may be written as "A,B,0,2,0,3" which would be incorrectly interpreted as six columns by ARSDA. I will fix this problem in the next release. For the moment, just change your Windows' number notation as follows:

  1. Press Window-x and click 'settings'
  2. Click 'Time & language', and then 'Additional date, time, & reginal settings'
  3. Under 'Region', click 'Change date, time, or number formats'
  4. Click 'Additional settings', and change 'Decimal symbol' to '.' and 'List separator' to ','
  5. Click 'OK'.
For Windows 64-bit computers:
The following prerequisites are required:
  • Windows Installer 4.5
  • Microsoft .NET Framework 4 Client Profile (x86 and x64)
If these components are already installed (almost certainly true, unless you are still running Windows XP, you can launch the application now. Otherwise, install prerequisites and run the application.
For Macintosh computers:
  1. (If you are already developing .NET programs on your MAC, then you may go directly to #4)
  2. Install wine for Mac computers (You could install mono to run ARSDA without Wine)
  3. At the end of installation, wine will automatically prompt you to instlal Mono. Acept to install
  4. Download and unzip ARSDA_Mac.zip to a directory, say ~/ARSDA
  5. Open a terminal windows and type the following commands:
    sudo apt-get install mono-vbnc (Otherwise you may encounter 'Mono error: The entry point method could not be loaded')
    cd ~/ARSDA
  6. Installation is now complete. Type mono ARSDA.exe to run.
  7. Here are some screenshots of ARSDA on Mac
For 64-bit Linux computers:
  1. Click the App Store or Package Manager, and choose wine to install (You could install mono to run ARSDA without Wine).
  2. At the end of wine installation, you will be prompted to instlal Mono. Acept to install
  3. Download and unzip ARSDA_Linux64.zip to a directory, say ~/ARSDA.
  4. Open a terminal windows and type the following commands:
    sudo apt-get install mono-vbnc (Otherwise you may encounter 'Mono error: The entry point method could not be loaded')
    cd ~/ARSDA/NCBI
    chmod 755 *
    cd .. (change back to the ARSDA directory where ARSDA.exe is located)
  5. Installation is now complete. Type mono ARSDA.exe to run.
  6. Here are some screenshots of ARSDA on Ubuntu

Source code in VB2013 (Please read the following before downloading)

  1. I support only the unmodified version
  2. This site (http://dambe.bio.uottawa.ca/ARSDA/ARSDA.aspx) is the only site to release source code
  3. Please let me know how you improved ARSDA in detail so that I can approve the change, acknowledge your contribution, and release a new version

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