Week 3 Assignment

[msiqi]

Part 1: Bash script for Exercise 1 (2.5 pt)

Evaluation:

• Question 1.1 +0.5 pt Good use of awk. Assuming uniform read lengths, it might have been faster to just get the length of the second line for the first read by using head -2|tail -1 and then piping that into either awk or wc -m
• Question 1.2 +0.5 pt
• Question 1.3 +0.25 pt Used incorrect read length to calculate coverage
• Question 1.4 +0.5 pt
• Question 1.5 +0.5 pt include command to run fastqc on ALL the fastq files

Score: 2.25/2.5 pt

Part 2: Bash script for Exercise 2 (3 pt)

Evalutation:

• Question 2.1 +0.5 pt
• Question 2.2 +0.5 pt
• Question 2.3 +0.5 pt This is the right command to obtain number of alignments, though you should have gotten 17815 as a result...
• Question 2.4 +0.5 pt
• Question 2.5 +0.5 pt
• Question 2.6 +0.5 pt

Score: 3/3 pt

Part 3: Python script for Exercise 3 (2.5 pt)

Evaluation:

• Well-written python code and methods to obtain appropriate indices for data

Score: 2.5/2.5 pt

Part 4: R script and figures for Exercise 3 (2 pt)

Evaluation:

• Don't have to push .txt files as these are lengthy
• Histogram plots look good and have meaningful interpretations of the distribution that show understanding of the dataset and what is being measured

Score: 2/2 pt

Total score: 9.75/10 pt