Question: When should the FastQC software be used to QC 10x data?
Answer: You may wish to run FastQC if you suspect poor sequencing quality or have some 'N's in the barcodes. Low valid barcodes also result in a certain loss of reads, thus a low median gene count per cell. In such cases, using a third-party tool to generate a quality control report is helpful to assess the quality of the data. For instance, generating a FastQC report on the raw sequencing data (i.e. FASTQ files) can be done as a routine quality control check after receiving the data from a high throughput sequencing run.
Here is an example syntax to run FastQC:
fastqc -t 8 -f fastq -o ./output_directory_name/ /path_to_fastq_files_dir/*.gz
The example above uses the downloaded FastQC executable file (fastqc), the number of threads for the program to use (-t), the input file type (-f), an output directory name to save the FastQC reports to a location other than the current directory (-o), and the full path to the input FASTQ files.
More details on how to download, install, and execute FastQC can be obtained from the links below:
Download FastQC: https://www.bioinformatics.babraham.ac.uk/projects/download.html#fastqc
Install FastQC: https://raw.githubusercontent.com/s-andrews/FastQC/master/INSTALL.txt
Note FastQC can also be installed and run as a "click-and-go" Desktop application on your Windows/Linux FastQC v0.11.9 (Win/Linux zip file) or MacOS personal computer FastQC v0.11.9 (Mac DMG image).