Miseq Prokaryote FASTQ analysis

Introduction

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.

Procedure

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.

   #!/bin/bash
   #$ -cwd
   #$ -j y
   #$ -S /bin/bash
   #$ -V
   #$ -q marvin.q
   # some quick "argument accounting"
   EXPECTED_ARGS=1
   if [ $# -ne $EXPECTED_ARGS ]; then 
   echo "error, this script should be fed with one argument: a filelist of fastq(.gz) files"
   exit
   fi
   module load FASTQC
   N=( $(sed -n "${SGE_TASK_ID}p" $1) )
   R1=${N[0]}
   R2=${N[1]}
   # echo "fastqc $R1 $R2"
   fastqc $R1 $R2