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.