Miseq Prokaryote FASTQ analysis

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We have our own Miseq machine and each week a run is carried out (each run costs about £1000 in consumibles) from various samples.

They are uploaded onto HDRIVE.


  1. Go into marvin scratch area and create a new directory, reflecting the date of the run.
  2. Make sure you have mounted the hdrive onto marvin.
  3. Create symlinks from your mounted directory to the new directory in $SCRATCH you've just created. An example is:
    for i in $(ls /storage/home/users/ramon/mnt/miseqda/2016-07-15_160715_M01714_0021_000000000-ANWN5/*.fastq.gz); do ln -s $i; done
  4. We need to generate a file listing of these files for later processing. The listing should reflect the paired nature of the fastq files, and if they are named properly this should not be a problem and can be created with
    ls *.fastq.gz > fq.lst
    followed by editing so that each line contains the pair appropriate pair of fastq files.
  5. then we can run a quality detection program, with the most widely used one being Babraham Institute's FASTQC. The following script will do each fastqc pair in parallel.
    #$ -cwd
    #$ -j y
    #$ -S /bin/bash
    #$ -V
    #$ -q marvin.q
    # some quick "argument accounting"
    if [ $# -ne $EXPECTED_ARGS ]; then 
    echo "error, this script should be fed with one argument: a filelist of fastq(.gz) files"
    module load FASTQC
    N=( $(sed -n "${SGE_TASK_ID}p" $1) )
    # echo "fastqc $R1 $R2"
    fastqc $R1 $R2