September 2019
Differential Gene Expression Analysis Workflow
Fastq file format
Fastq file format - Headers
Fastq file format - Sequences
Fastq file format - Quality Scores
QC is important
Check for any problems before we put time and effort into analysing potentially bad data
- Start with FastQC
- Quick
- Outputs an easy to read html report
We run fastQC from the terminal with the command
fastqc <fastq>
but there are lots of other parameters which you can find to tailor your QC by typing
fastqc -h
Per base sequence quality
Good Data
Bad Data
Per base sequence content
Good Data
Bad Data
Per sequence GC content
Good Data
Bad Data
Adaptor content
Good Data
Bad Data
