Chapter 11 Exercise 2

The directory "~/Linux/6_final_exercise/" has all the files you need. Below is a set of tasks and questions that will require all the skills you have gained from this practical.

1. See what files are in the directory.
   
2. Rename the file "3-P£_CACTTCGA_L001_R1_001.fastq" as "3-P3_CACTTCGA_L001_R1_001.fastq".
   
3. Make a backup of the files in a directory called backup.
   
4. How many reads are in the samples?
   
5. Remove the fastq files with no data.
6. Update the backup files with the previous change.
   
7. Check if the 1st read names match in the paired files.
   
8. Check if the last read names match in the paired files.
   
9. In file "1-P1_ATGCCTGG_L001_R1_001.fastq" look for sequence headers with the term ‘psychrobacter'. (Tip: Use grep)
   
10. In the sample 1-P1 remove any fastq entries where the term ‘psychrobacter’ appears in the fastq header. Do this for the R1 and R2 files.
    
11. Print to screen the fastq header, sequence and quality data for the 25th sequence in sample 2-P2 for both the R1 and R2 file. Do this with one command for R1 and a separate command for R2.

You can check my solutions in the Answers section. These are not the definitive solution but only examples of solutions. If your method works and you understand why then you have done it correctly.