Code challenges to be completed in class during lecture
##Introduction to commandline
Code challenge 0a - commandline grammar
Code challenge 0b - reading a code box ##Files, directories, editing and pipes
Code challenge 1 - listing bioinfo software
Code challenge 2 - counting sequences in a fasta file
##Running programs (from the Beocat head node as well as the queue), Shell scripts
Code challenge 3 - loops to prepare raw data
Code challenge 4 - convert new Illumina data and use existing code in your own new script
##Perl scripts
Code challenge 5 Write a simple Perl script that runs a Oases transcriptome assembly.
Code challenge 6 Modify the Oases transcriptome assembly script to loop over all odd k-mer values within a user-defined range.
Code challenge 7 Write a Perl script to count the A's, C's, G's, T's or IUPAC ambiguous bases are in a fasta file.