Tutorial directories
I use a standard layout for directories in the UPARSE tutorials as shown in the table below. Here, tutname stands for the name of the tutorial, e.g. misop or hmptut.
| Directory name | Contents |
| tutname/scripts/ | Bash scripts. You need Bash and a few basic Linux commands to run the tutorials. Bash is standard in Linux and OSX. Under Windows, Cygwin provides an excellent Linux-like environment including bash. |
| tutname/py/ | (If needed). Python scripts. Some scripts may not run under Python v3.x, in which case try v2.x. |
| tutname/fq/ | Reads in FASTQ format. |
| tutname/ref/ | Reference database(s) specific to a particular dataset, if needed. Does not include general-purpose reference data such as a UTAX database. |
| tutname/out/ | Output files. The download contains the output files I made when I ran the scripts. You can regenerate them using the Bash script(s) with names like run_uparse.bash. |
Note that the tutorial scripts assume that they are being run with tutname/scripts as the current directory.
The tutorial tarball files (.tar.gz) have this directory structure. After downloading, make a top-level directory for the tutorials, change to that directory, and extract files from the tarball, something like this:
mkdir ~/tutorials
cd ~/tutorials
tar -zxvf ~/Downloads/tutname.tar.gz
I will assume your top-level directory is ~/tutorials when I need to show an example command, but you can put this directory anywhere you like.
The tilde (~) in a directory name is an abbreviation for the user's home directory, e.g. /home/robert. You don't have to put the tutorial files there, I'm just using it as an example.