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Extut tutorial MiSeq 2x250 PE reads, "Extreme" mock community sample |
Comparing the UPARSE and UNOISE pipelines on species >97% similar
This tutorial uses data from the "Extreme" mock community described in the DADA2 paper. I took a subset of 50k reads from SRR2990088 using the fastx_subsample command
Download the utorial files: extut.tar.gz.
I'll assume your downloaded files are in ~/Downloads, if you downloaded to a different path then replace as needed below.
Make a top-level directory for the tutorials, change to that directory and extract the data files using tar for the tutorial files. See tutorial directories for description of subdirectories.
Extract the data files from the archives:
mkdir -p ~/tutorials
cd ~/tutorials
tar -zxvf ~/Downloads/extut.tar.gz
Set the $usearch environment variable to the path name of your usearch binary file.
Install the sintax referennce database by running the setup_sintax.bash script, like this.
cd ~/tutorials/misop/scripts
./setup_sintax.bash
Notice the dot and slash (./) before setup_sintax.bash. This tells the shell to look for the command file (script or binary) in your current directory (dot means current directory). This is needed if the current directory is not in your PATH. Tutorial scripts always assume that they are being run like this, i.e. from inside the scripts/ subdirectory.
The setup_sintax.bash script uses curl to fetch the data. Some systems don't have curl in which case you can use wget. There is a wget command in the script which is commented out so it's a simple edit of the script to comment out curl instead.
There run.bash script runs the UPARSE and UNOISE pipelines. Most of the commands for UPARSE and UNOISE are the same, so I combined them into one script that does both.
Run the pipeline script like this:
cd ~/tutorials/extut/scripts
./run.bash
This should reproduce the pre-computed files in the extut/out/ directory.