fastqc_multiqc.md

FASTQC and MultiQC

FASTQC and MultiQC are two tools for performing quality control (QC) of sequence read data (fastq files). The most important things to know:

• FASTQC is a program that is run on individual fastq or fastqc.gz files. It compiles basic statistics about read quality and base pair frequencies. Note that some of the quality checks are more appropriate for DNA-seq than RNA-seq. So just because you see a warning from a FASTQC report doesn't mean there is a problem.
• MultiQC is a program that aggregates statistics across many files, and many programs. If you run this program in a directory, it will search for files it recognizes and build an HTML report that summarizes all the information.

Both programs are available on the cluster. Just run:

module load fastqc
module load multiqc

How to incorporate into an RNA-seq workflow, see the following Snakemake file, which will perform FASTQC, Salmon quantification, and MultiQC report building all together:

https://gist.github.com/mikelove/5a8134e57f652f970f1a176efc900cbe#file-snakefile_with_qc

Note that you need to first create the directories quants, qc, and multiqc.

You could then run this program from the command line with, e.g.:

snakemake -j 4 --latency-wait 30 --cluster "sbatch -n 12 -N 1 --mem=10000 --time 60"

which would submit 4 jobs at one time to the cluster, each with 12 cores.