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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.