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assignments:2018assignment4

Assignment 4

Due Sept 6, 2018

:!: Note new due date!!!

Compile your answers in a .txt document

Turn your answers by uploading your .txt document to CANVAS

:!: HINT: If the question asks for a command, write the full command as you would write it on the command line.

:!: HINT: You don't need to include the question in your write-up, just the answer.


Question 1

  • Download this gtf file of annotations of the yeast genome: saccer3_annotation.gtf.gz
  • The following line of piped code counts some type of feature in the .gtf file.
$ cut -f 9 saccer3_annotation.gtf | cut -d ';' -f 1 | sort | uniq | wc -l
  • A. What type of feature is being counted?
  • B. Explain what each step of the piped code does.

Question 2

  • Let's continue to workw ith your file called saccer3_annotation.gtf.gz.
  • The third column contains feature type information.
  • A. What piped command will display the unique names of feature types included in your file (i.e.: CDS, exon, etc)?
  • B. Can you do the same thing, display the unique names of feature types, but this time instead of using piped commands, can you use sequential commands that save each step to a temporary file? Write the commands.

Question 3

  • A. Which node(s) on SUMMIT do you log into?
  • B. Which node(s) on SUMMIT can be on when you submit sbatch commands?
  • C. Which node(s) on SUMMIT do you request to use to perform large computations?

Question 4

  • For this question, use the bash script below called bowtie_align.sh
#!/usr/bin/bash

#SBATCH --job-name=bowtie
#SBATCH --nodes=1
#SBATCH --ntasks=1
#SBATCH --partition=shas-testing
#SBATCH --qos=testing
#SBATCH --time=0:30:00
#SBATCH --output=out_bowtie_%j.log

hostname

# compresses a genome
bowtie -p 1 file.fastq 
  • A. Which line of code (copy and paste) will execute a bowtie alignment?
  • B. Which line of code (copy and paste) tells slurm how long to allot for the job to proceed?
  • C. Which line of code (copy and paste) is a comment code for the human programmer to read.
  • D. What is the purpose of this line #SBATCH –ntasks=1?

Question 5

  • List the commands you would use to…
    • A. Log into summit
    • B. Move from the login node to a compile node
    • C. Execute a job called bowtie_align.sh using slurm to send the job to a compute node
    • D. Check the status of your job

Fun Stuff

  • For this question, in the script below, what does this mean #SBATCH –output=out_bowtie_%j.log ?
#!/usr/bin/bash

#SBATCH --job-name=bowtie
#SBATCH --nodes=1
#SBATCH --ntasks=1
#SBATCH --partition=shas-testing
#SBATCH --qos=testing
#SBATCH --time=0:30:00
#SBATCH --output=out_bowtie_%j.log

hostname

# compresses a genome
bowtie -p 1 file.fastq 
  • How would you have summit e-mail you when your jobs are complete?
assignments/2018assignment4.txt · Last modified: 2018/08/30 14:08 by erin