FASTQ Quality controls

Using FastQC you can perform the necessary controls over FASTQ files.

fastqc C51C3ACXX_TC1-H3K4-A-D3_14s006647-1-1_Sinkkonen_lane514s006647_sequence.txt.gz

but one file at a time, does not benefit the HPC.

running in parallel

If you have booked at least 4 cores, otherwise update the -j option:

parallel -j 4 "fastqc {}" ::: fastq/*.gz

the {} instruction will be replaced by all occurrences of the pattern *.gz, everything that ends by .gz. parallel takes care of submitting a new job so the number of parallel remains the same.

running serial (for information)

A tidy bit of bash programming to do it for all files NOT in parallel

for f in *.gz
  do fastqc $f
done

visualize the results

collect the html files using either rsync, scp for command lines or FileZilla for a GUI tool.

You should observe some issues that needs to be solve.