Difference between revisions of "Miseq Prokaryote FASTQ analysis"
| Line 10: | Line 10: | ||
# 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> 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> for i in $(ls /storage/home/users/ramon/mnt/miseqda/2016-07-15_160715_M01714_0021_000000000-ANWN5/*.fastq.gz); do ln -s $i; done</pre> | ||
| − | # then we can run a quality detection program, with themost widely used one being FASTQC. The following script will do each fastqc pair in parallel. | + | # then we can run a quality detection program, with themost widely used one being FASTQC. The following script will do each fastqc pair in parallel.<pre> |
| − | |||
#!/bin/bash | #!/bin/bash | ||
#$ -cwd | #$ -cwd | ||
| Line 19: | Line 18: | ||
#$ -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 $EXPECTED_ARGS ]; then | ||
| Line 30: | Line 29: | ||
R2=${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
- Go into marvin scratch area and create a new directory, reflecting the date of the run.
- 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:
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
- 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.
