Page Comparison

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To log in to the Atmosphere virtual machine, do the following:

1. Go to www.https://atmo.iplantcollaborativecyverse.org./
2. Log in using your iPlant CyVerse credentials.
3. After clicking launch New Instance, look for STACKS Ubuntu 16 Stacks 1.23 v146 v.2.0, and then select it.
4. Under instance type, select tiny2.
5. Click Launch Instance.

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Note: All staged data we will be using for this exercise are under /home/<your_cyverse_username>/stacks_demo.

1. Connect to the Atmosphere image. (Detailed instructions are located here https://pods.iplantcollaborative.org/wiki/display/atmman/Logging+In+to+an+Instance.)
2. From the command line use “mkdir” to create a folder were we will work and save our work):
   cd ~
   mkdir ~/stacks_demo
3. After that use “cd” command to move into the newly created directory.
   cd stacks_demo

Clean and demultiplex the data

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1. Within the stacks_demo directory, create a subdirectory called “demultiplex_samples” by using:
   mkdir demuplix_samples
2. 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

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