qc_summary
Report the mean quality score per base from the output of FastQC.
FastQC is used in bioinformatics as a quality control tool for high throughput sequence data. qc_summary.sh takes FastQC's output and reports the mean quality score per base.
Input
FastQC creates an HTML file and a ZIP file per sample, for example sample1_fastqc.zip. qc_summary.sh takes the ZIP files, looks for a file named fastqc_data.txt inside, then extracts the information in the section labeled "Per base sequence quality pass":
Per base sequence quality pass
#Base Mean Median Lower Quartile Upper Quartile 10th Percentile 90th Percentile
1 32.94 34.0 34.0 34.0 32.0 34.0
Output
qc_summary.sh creates a tab-separated value (TSV) file named qc_summary.tsv. Here is an example of its contents:
Base sample1_1 sample1_2 sample2_1 sample2_2
1 32.94 32.90 33.01 33.25
Variables
Prior to running qc_summary.sh, some variables require editing:
input_prefix='CB'
For example, let's say our inputs are named like:
- CB9_KO_b-min_S9_R1_fastqc.zip
- CB9_KO_b-min_S9_R2_fastqc.zip
- CB10_KO_b-pos_S10_R1_fastqc.zip
- CB10_KO_b-pos_S10_R2_fastqc.zip
- CB11_PA01_a_S11_R1_fastqc.zip
- CB11_PA01_a_S11_R2_fastqc.zip
In this case, CB is the correct prefix to use.
input_sort_key='1.3'
This ultimately effects the ordering of the samples in the output file. In our example above, we want to sort by the first three characters: CB followed by a number.
Usage
- Place qc_summary.sh in the same directory as the ZIP files
- In a terminal: bash ./qc_summary.sh
Prerequisites
- Bash
Tested On
- Ubuntu 16.04 LTS
- RHEL 6,7
Built With
- Bash - Programming language
License
This project is licensed under the MIT License - see the LICENSE.md file for details.