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 n scrathc 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