exercises.md

Exercise 1: "Quality trimming on 6 Fastq files, in serial with multithreading"

• Log into Orchestra using Terminal or Putty or Git BASH
• Start an interactive session with a single core
• Change directories into the ~/unix-intro/, and move the trimmomatic-serial.lsf file/script from the other directory to your current directory (~/unix-intro/)
• Open the script with nano
• Modify the LSF (bsub) directives to use only 4 cores
• Add a bsub directive to make sure that you get an email when the job completes
• Submit the script to the LSF queue using bsub (Hint: Job submissions use special syntax and just bsub scriptname.lsf will not work)
• Once submitted, immediately check the status of your job. How many jobs do you see running? Is there a difference in the "Queue" on which they are running?
• When the job is completed it will create a new directory with new files: What is the name of the new directory? How many new files and directories were created within it?
• List only those files that end in .zip,

Exercise 2: "Quality trimming on 6 Fastq files, in parallel with multithreading"

• Check and make sure you have an interactive session going and also that you are in the ~/unix-intro/ directory.
• Copy over the trimmomatic-on-input-file.sh and trimmomatic-multithreaded.sh files from the other directory to your current directory
• Use nano to open the trimmomatic-multithreaded.sh file and make note of the bsub submission command in it. Is this a file that can be submitted to LSF using bsub < scriptname?
• Run trimmomatic-multithreaded.sh using sh instead of bsub <
• How many job submission notification did you get?
• Once submitted, immediately check the status of your jobs. How many are running and how many are pending?
• Once again, when the job is complete a new directory with new files will be created. Use ls -l to determine if the same output was generated for both.
• What do you think the advantage is of running the job(s) this way as compared to Exercise 1?