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. then we can run a quality detection program, with themost widely used one being 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 # change value to suit!
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