Difference between revisions of "Miseq Prokaryote FASTQ analysis"

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# Make sure you have mounted the hdrive onto marvin.
 
# Make sure you have mounted the hdrive onto marvin.
 
# Create symlinks from your mounted directory to the new directory in $SCRATCH you've just created. An example is:<pre>&#10;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</pre>
 
# Create symlinks from your mounted directory to the new directory in $SCRATCH you've just created. An example is:<pre>&#10;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</pre>
# 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.
+
# 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.<pre>&#10;
 
 
 
  #!/bin/bash
 
  #!/bin/bash
 
  #$ -cwd  
 
  #$ -cwd  
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  #$ -q marvin.q
 
  #$ -q marvin.q
 
   
 
   
  # some quick "argument accounting"
+
  # some quick "argument accounting"<pre>
 
  EXPECTED_ARGS=1 # change value to suit!
 
  EXPECTED_ARGS=1 # change value to suit!
 
  if [ $# -ne $EXPECTED_ARGS ]; then
 
  if [ $# -ne $EXPECTED_ARGS ]; then
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  R2=${N[1]}
 
  R2=${N[1]}
 
  # echo "fastqc $R1 $R2"
 
  # echo "fastqc $R1 $R2"
  fastqc $R1 $R2
+
  fastqc $R1 $R2</pre>

Revision as of 16:40, 18 July 2016

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"<pre> 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