RNA-seq analysis in R

QC of raw reads with FastQC - Solutions

Exercise 1

1. 1. Check the location of the current directory using the command pwd
      
   2. If the current directory is not /home/participant/Course_Materials, then navigate to the Course_Materials directory using the cd (change directory) command:
      cd ~/Course_Materials
2. 1. Use ls to list the contents of the directory. There should be directory called fastq
      
   2. Use ls to list the contents of the fastq directory:
      ls fastq

3. Create a new directory for the QC results called QC using the mkdir command:
   mkdir QC

4. Run fastqc on one of our samples:
   fastqc fastq/MCL1.DL.fastq.gz

5. The previous command has written the report to the fastq directory - the default behaviour for fastqc. We want it in the QC directory.
   1. Use the rm (remove) command to delete the report:
      rm fastq/MCL1.DL_fastqc.html
      
   2. Also delete the associated zip file (this contains all the figures and data tables for the report)

rm -f fastq/MCL1.DG_fastqc.zip

6. Run the FastQC again, but this time try to use the -o option to have the report written to the QC directory.

fastqc -o QC fastq/MCL1.DL.fastq.gz

7. Open the html report in a browser and see if you can answer these questions:
   A) What is the read length? 100
   B) Does the quality score vary through the read length?
   Yes, the first few bases and the last few bases are typically of lower quality.
   C) How is the data’s quality?
   Overall, pretty good.