I am completely new to bioinformatics so I'm looking to learn how to do this.
I have multiple directories with fastq files: E.g; 10 Directories with each time series, each with Treatment and control directories, each with rep1 rep2 rep3.
For example: T9/Infected/Rep1/*.fastq.gz.
I'm looking to create a loop to run fastQC on each fastq file instead of having to submit a separate job for each directory.
Then to either output the fastQC data to a single directory or if possible a directory corresponding to each rep - e.g. rep1 results go into a folder called rep1 and so on