Syllabus is available as a google doc.

Lectures will be linked here as they are available

Week 1 (F): Intro to command line, UNIX (Liu)
Week 2 (W): Intro to Perl, data structures in Perl [PDF] – strings, numbers, arrays, hashes (Stajich)
Week 2 (F) : Logic and loops [PDF] – if statements, while,for loops (Stajich)
Week 3 (W): Reading/Writing, References, Subroutines [PDF] [Example 1 – get data from web] [reference example] (Stajich)
Week 3 (F): Advanced UNIX (Liu)
Week 4 (W): Debugging, programming practices (Liu)
Week 4 (F): Objects, Modules (Liu)
Week 5 (W): BioPerl: Sequences, Databases (Stajich) – many example codes in the github repo and through website
Week 5 (F): Regular Expressions, [data link] BioPerl: BLAST parsing, Multiple alignments, Trees (Stajich)
Week 6 (W): Next Generation Sequence data (NGS) alignment, DNA-Seq, SNPs (Stajich) [PDF] – see DNA align and SNP calling example
Week 6 (F): Next Generation Sequence data RNA-Seq (Stajich) [PDF] – see RNA-seq pipeline example
Week 7 (W): Workflows: BLAST, Orthologs (Stajich) [PDF], code to make single linkage clusters and code to run OrthoMCL on biocluster (you need to edit this script and the config file after it is downloaded to give your unique database name)
Week 7 (F): Workflows: Orthologs, Multiple Sequence Alignment (Stajich) – see code for making ortholog group sequences written during class
Week 8 (W): NGS: small RNA-Seq (Liu)
Week 8 (F): NGS: Bisulfite sequencing (Liu)
Week 9 (W): NGS: ChIP-Seq (Liu)
Week 9 (F): Thanksgiving Holiday NO CLASS
Week 10 (W): Introduction to relational databases (Liu)
Week 10 (F): Using Perl to interact with databases (DBI) (Liu)
Week 11 (W): Presentations
Week 11 (F): Presentations

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