Contents

1 Last time:
2 Today: Download, QC and Preprocessing of Illumina data:
3 Login commands
4 Downloading precompiled software
5 Introduction to search path: $PATH
- 5.1 Where do we put the software after download?
- 5.2 Changing your path
6 What if binaries are not available for your OS?
- 6.1 Installing from source
7 Server operations: Using module to temporarily load functions:
- 7.1 Server operations: Running jobs in the background
- 7.2 Killing jobs
8 Downloading data from sra archive
9 Interpreting .fastq (.fq) format and Phred scores
- 9.1 Inspecting data
10 QC and preprocessing
11 FastQC: quality control for .fastq files
- 11.1 In class exercise 1: FastQC
12 Answers to in class exercises
- 12.1 In class exercise 1 (answers): FastQC

1 Last time:

Running interactive sessions
submitting job with sbatch
introduction to apt-get and brew package managers
Used apt-get or brew to install the sratoolkit on your local macine.

2 Today: Download, QC and Preprocessing of Illumina data:

downloading bowtie2 binaries
adding directories to the $PATH
Using fastqc to check the quality of library or sequencing run.
Using command line tools to pre-process .fastq data.