NSCI 580A4

Instructors
Tai Montgomery
Erin Nishimura

wiki:exercises2

# FURTHER EXERCISES 160830

### Exercise 1

• Let's work with the .gff file that is in your directory, S288C_reference_genome_R64-1-1_20110203/03_annotations. It is called saccharomyces_cerevisiae_R64-1-1_20110208.gff
• Use head and tail to look at the .gff file saccharomyces_cerevisiae_R64-1-1_20110208.gff.
• Use redirection to save the first 100 lines of saccharomyces_cerevisiae_R64-1-1_20110208.gff as a file called sacCer3_first100.gff.
• Use redirection to save the last 100 lines as sacCer3_last100.gff.

### Exercise 2

• Start within a directory that contains the sub-directory 02_fastafiles. Redirect the output from ls 02_fastafiles/ to a file.
• Redirect the stderr message from ls doesnotexist to a file.
• Redirect the stdout and stderr messages from the command ls 02_fastafiles/ doesnotexist to a file.

### Exercise 3

• Let's work with the .gff file that is in your directory, S288C_reference_genome_R64-1-1_20110203/03_annotations. It is called saccharomyces_cerevisiae_R64-1-1_20110208.gff
• Use grep to find all the lines that contain a #.
• Next, use 'grep' for the same operation, but this time display the line number as well.
• Make a file out of saccharomyces_cerevisiae_R64-1-1_20110208.gff that contains ONLY the annotation material. The annotation material is any line that starts with # or ## or ###.
• Make a file that contains NO annotation material.

### Exercise 4

• Use wc to save a file containing word count information for one file.
• Try to use cut to parse the word count information (in your saved file) into lines, words, and characters. It doesn't work.
• Open the file in your text editor. Can you figure out why you couldn't parse columns using cut?