These are files which will be used for teaching purposes in SLE712 Bioinformatics and Biotechnology at Deakin University.
These are some Sanger sequencing files used in 2019 but not for 2020.
This folder contains mydata.tsv, gene_expression.tsv and growth_data.csv. We will work with the mydata.tsv file in class to demonstrate how to properly read a system file into R. The other two files gene_expression.tsv and growth_data.csv will be used by students to answer questions asked in assignment 3 part 1. This part of the assignment is designed to test students ability to read files into R and perform ordering, subsetting, and create simple charts.
This folder contains example.fa, create_fasta.sh, sample.fa, mutblast_functions and unwrap_fasta.pl. create_fasta.sh is a shell script called that samples 20 random E. coli gene sequences. The sample.fa file is a multi fasta file containing 20 randomly selected E. coli gene sequences. The names of the sequences in sample.fa have been removed because it is part of the exercise for students to figure out to what gene these sequences belong. In class we will work together to analyse a sequence in the example.fa file. The mutblast_functions.R file contains some handy functions that students should use in their assignment to perform random mutagenesis of a sequence and to perform a blast search. The unwrap_fasta.pl file is a perl script to unwrap a fasta file. This part of the assignment is designed to test more advanced skills including using randomisation tools, using BLAST, performing simulations and interpreting data.
This covers the answers to the take-home questions for prac 1.
This is an Rmarkdown document that revises work done in prac 2 where we began working with version control, code documentation and Rmarkdown.
This is an Rmarkdown document will be covered in prac 3.
In this prac we will be applying everything we've learned to begin analysing sequence data in R.