Content Comparison

UNIX and HPC exercises

Answer key can be found here.

# Logging in and starting an interactive job

1. Log into Orchestra O2 and start a single core interactive job.

# Practicing Unix commands and using vim

2. Make a new directory called homework inside your ~/ngs_coursechipseq directory. Change directories to your homework directory.

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• What is the absolute path of your current directory?
• Copy both of the Mov10_kd files to the homework directory inside of your ~/ngs_coursechipseq directory. 

5. Change directories to your home directory. Locate and enter the raw_data folder (Hint: this was from the rna-seq portion of Session I).

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• How many reads were obtained for this sample?
• What was the command you used for determining the number of reads in your file?

# Practicing more advanced commands, including for_loops, redirection, scripts.

7. Using the pipe command from the previous question, write a for_loop to determine the number of reads obtained for every fastq sample in the homework folder.

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• Upload the mov10_fastq_reads.txt script to your folder on the course wiki homework page (see link above).

# Practicing FastQC

10. Exit the interactive session (compute node) and go back to the login node (loge or mezzanine).

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• Use Filezilla to download the zipped files to your own computer and examine the FastQC reports.
• Which samples have quality scores that drop below a score of 25?
• Do any samples have adapter contamination based on the information in the FastQC report?
• Upload the hw_fastqc_run.lsf script to your folder on the course wiki homework page (see link above).
  

# Metadata

11. Enter the rnaseq folder, and create a README file (hint: use vim to create the file), as described in the Exercise section of the Data Management lesson. Give a short description of the project and brief descriptions of the types of files you will be storing within each of the sub-directories.

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• to your folder on the course wiki homework page (see link above).