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Course Catch-up Day (L17)

Instructions for Wednesday, March 5th

For today’s class, we will use this session as a course catch-up and troubleshooting day.

If you can answer “yes” to all the following questions, you do not need to attend class as no new materials will be discussed. This time is provided as additional support for guided troubleshooting.

  1. Have you successfully downloaded the publicly available dataset for your final project? Note: This is not required yet, but several students have encountered issues.

  2. Can you confidently copy data from the shared course directory to your working directory during class?

  3. Are you comfortable writing and submitting scripts using the SLURM job submission system?

  4. Can you transfer files between the VACC and your local desktop without errors?

  5. Can you independently create and submit scripts for the following tools:

    • rseqc
    • fastqc
    • trimmomatic
    • multiqc (to summaize outputs)

  6. Can you interpret a multiqc report and identify potential quality concerns?

  7. Do you know how to:

    • Check job status
    • Cancel a job
    • View job output and/or error logs

  8. Is your project directory organized in a clear structure? Could you use some suggestions?

  9. Are your scripts saved and commented so you could rerun them using your samples?

If you are unsure about any of the above, I strongly encourage you to attend. This session is designed to provide 1-on-1 support during a time we are both available.