urwahnawaz / Quality-Control-

Codes used for assessing the quality of raw Illumina reads for the Giant Australian Cuttlefish

Quality Control

The codes were mainly used to clean up Illumina RNA-seq raw reads for my honours thesis project

Programs used

• FastQC - Assesses the quality of the data
• TrimGalore - Runs cutadapt and FastQC
• ngsReports - R package for managing FastQC output

Codes and description

• FastQC.sh: Runs FastQC on the initial data
• TrimGalore.sh: Runs TrimGalore
• codefortables.py: opens the summary.txt output file and makes LaTeX tables based on the results
• count_PE.sh: Runs the script count_fastq.sh on Phoenix HPC
• count_fastq.sh: Counts the number of reads in a .fq file
• fastqc_phoenix.sh: Runs FastQC on Phoenix
• run_ngsReports.R: Makes combined plots for the FastQC output