Check data quality with fastqc
fastqc is routinely used as a command-line program for assessing the quality of reads in raw fastq files. The program can be run on your laptop, but it will be much easier/faster to run on a server with more compute power.
Begin by using fastqc to check the quality of each of your fastq files.
# navigate to the folder with your raw fastq files # run fastqc on all files, putting the outputs into a new folder called 'fastqc' fastqc *.gz -t 24 -o fastqc
Summarize QC results with MultiQC
MultiQC is a fantastic piece of software for aggregating and summarizing the outputs from many different kinds of bioinformatics programs in one convenient and interactive html file. In this case, we’ll use it to summarize the output from fastqc.
# change to the directory with your fastqc outputs # run multiqc with the -d command to tell multiqc to look in all folders (data, analysis and qa) to find log files multiqc -d .
You should now see a multiqc_report.html file in your project directory. You can copy this file from our server to your local computer using an FTP client (e.g. FileZilla), then double click and explore!