Simple Instructions
If you have an xml settings file (called say Settings.xml) and a fastq data file (say Data.fastq) you can run the analysis simply by typing the following.
freqout.exe -xml=Settings.xml Data.fastq
or if you have a gzipped fastq file (saves hard disk space):
freqout.exe -xml=Settings.xml Data.fastq.gz
This will produce a file called "Results.csv" with a summary of the analysis. Multiple fastq data files can be specified in the command line simply by providing additional arguments for each file.
freqout.exe -xml=Settings.xml Data.fastq Data2.fastq Data3.fastq
Alternatively, to process multiple files simultaneously you can specify a directory that contains all of the files with the -d option. Any file in that directory with a .fastq extension will be analyzed.
freqout.exe -xml=Settings.xml -d="C:\MyDataDirectory\"
Note that on Linux and Apple computers you must invoke the mono command first, see more about this here.
Longer Instructions
The first thing to do to run the console application is to download the files as a zipped folder from the downloads page. You can unzip this folder which contains the executable freqseqc.exe and the library file freqseq.dll. You will be running the program from the command prompt (on windows, go to Start->Run and type "cmd.exe" followed by enter.
In order to run the program in the command prompt you have three options.
- Add the folder location with afseqc.exe to the path environmental variable.
- Fully specify the location of the file when typing the command, meaning type C:\SomeFolder\freqout.exe
- Copy the files freqout.exe and FreqSeq.dll to the folder with your fastq file, navigate to that folder in the command prompt using the
Copy both of these files to a directory of your choosing, and remember both of these files must be in the same directory for the program to work. Note that these instructions are a standard step for any command line program installation and should be easy. If they are confusing or new to you don't hesitate to ask a computer savy friend or feel free to contact us. You may also find the GUI program far simpler to use if this is the case.
Once you can access the program on the command prompt, you can see more about it by using the -help command.
freqout.exe -help
The only required option is for the xml file
-xml Name of the XML settings file.
Other options that are available are:
-v Makes the program produce verbose output during analysis.
-d Specifies a directory to search for .fastq files in.