To log in to the Atmosphere virtual machine, do the following:
- Go to www.https://atmo.iplantcollaborativecyverse.org./
- Log in using your iPlant CyVerse credentials.
- After clicking launch New Instance, look for STACKS Ubuntu 16 Stacks 1.23 v146 v.2.0, and then select it.
- Under instance type, select tiny2.
- Click Launch Instance.
Note: All staged data we will be using for this exercise are under /home/<your_cyverse_username>/stacks_demo.
- Connect to the Atmosphere image. (Detailed instructions are located here https://pods.iplantcollaborative.org/wiki/display/atmman/Logging+In+to+an+Instance.)
- From the command line use “mkdir” to create a folder were we will work and save our work):
- After that use “cd” command to move into the newly created directory.
Clean and demultiplex the data
- Within the stacks_demo directory, create a subdirectory called “demultiplex_samples” by using:
- From the stacks_demo directory, execute the following command:
process_radtags -p ~/home/stacks_demo/fastq_files/ -o ~/stacks_demo/demultiplex_samples/ -b ~/stacks_demo/61VBPAAXX_key.txt -e apeKI -r -c --q