bioinfoipec/fastqc repository overview

⁠FastQC

This image facilitates the usage of FastQC⁠, a quality control tool for high throughput sequence data.

⁠Using the FastQC image

You should adapt and run the following command: docker run --rm -v /your/data/dir:/data bioinfoipec/fastqc fastqc /data/input.fq

In this command, you should replace:

• /your/data/dir to point to the directory that contains the FASTQ file you want to analyze.
• input.fq to the actual name of your input file.

To see the FastQC help, just run docker run --rm bioinfoipec/fastqc fastqc --help.

⁠Test data

To test the previous command, you can download this FASTQ compressed file⁠ (1.1GB). Note that it does not need to be decompressed as FastQC can deal with both compressed and uncompressed FASTQ files.

In the previous command you just need to replace /data/input.fq with /data/sra_data.fastq.gz. You can also speed up the execution by adding -t 4 to tell FastQC to use 4 cores (it uses 1 core by default). This command will produce two files containing the FastQC reports in the /data directory: sra_data_fastqc.html and sra_data_fastqc.zip.