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'.

If your Windows PC already has .NET 8 installed, download and run ARSDA.msi, otherwise download and run Setup.exe

1. Download ARSDA.msi
2. Download Whisky and unzip it.
3. (Let me know if the Whisky link above becomes unavailable)
4. Follow the concise instructions
5. When you see "ARSDA" with a green arrow above, double-click "ARSDA" and wait for 10 seconds (only for the first time) during which there seems no response, but ARSDA will eventually start.

1. Click the App Store or Package Manager, and choose wine to install.
2. (alternatively, issue the command sudo apt install --install-recommends winehq-stable)
3. At the end of wine installation, you may be prompted to instlal Mono. Acept to install
4. Download ARSDA.msi
5. wine msiexec /i ARSDA.msi
6. ARSDA is now ready to run.
7. Here are more information on msiexec
8. Here are some screenshots of ARSDA on Ubuntu