Return to the Course Home Page

TLDR Portfolio Assistance Week 4

A/Prof Olin Silander

Purpose

Purpose

TLDR summary of how to approach to Portfolio Assessment from Week 4.

1. Find a way to get the GC content and any other useful info from the fastq.gz sequence files using fx2tab
2. Write the output to a file; this will automatically be in tabbed column format.
3. Import the data (i.e. file) into R; read.table() is one possibility. read.table has a default expectation of tabbed column format
4. Make sure you know what the columns mean. You can rename them in the text file or using col.names=c("sequence-name", "length", "etc") within the read.table() line. You can also rename them after having read in the data using colnames(mydata) <- c("sequence-name", "length", "etc"). Note that in naming variables and column / row names, spaces are highly discouraged.
5. Look for correlations or patterns in the data: in Chrome, How can I look for correlations in data
6. Produce visualisations of your findings and explain/interpret them in a caption below the visualisaltion.