Miseq Prokaryote FASTQ analysis - Revision history

Rf at 17:01, 18 July 2016

2016-07-18T17:01:56Z

Rf at 16:47, 18 July 2016

2016-07-18T16:47:25Z

Rf at 16:46, 18 July 2016

2016-07-18T16:46:44Z

Rf at 16:43, 18 July 2016

2016-07-18T16:43:18Z

Rf at 16:40, 18 July 2016

2016-07-18T16:40:07Z

Rf at 16:29, 18 July 2016

2016-07-18T16:29:16Z

Rf at 16:27, 18 July 2016

2016-07-18T16:27:23Z

Rf at 16:26, 18 July 2016

2016-07-18T16:26:56Z

Rf at 16:24, 18 July 2016

2016-07-18T16:24:39Z

Rf at 16:16, 18 July 2016

2016-07-18T16:16:28Z

@@ Line 10: / Line 10: @@
 # 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 $i; done</pre>
-# We need to generate a file listing of these files for later processing. The listing should reflecte the paired nature of the fastq files, and if they are named properly this should not be a problem and can be created with<pre>&#10;ls *.fastq.gz > fq.lst</pre>
+# We need to generate a file listing of these files for later processing. The listing should reflect the paired nature of the fastq files, and if they are named properly this should not be a problem and can be created with<pre>&#10;ls *.fastq.gz > fq.lst</pre>&#10;followed by editing so that each line contains the pair appropriate pair of fastq files.
 # then we can run a quality detection program, with the most widely used one being Babraham Institute's FASTQC. The following script will do each fastqc pair in parallel.<pre>&#10;#!/bin/bash&#10;#$ -cwd&#10;#$ -j y&#10;#$ -S /bin/bash&#10;#$ -V&#10;#$ -q marvin.q&#10;# some quick "argument accounting"&#10;EXPECTED_ARGS=1&#10;if [ $# -ne $EXPECTED_ARGS ]; then &#10;echo "error, this script should be fed with one argument: a filelist of fastq(.gz) files"&#10;exit&#10;fi&#10;module load FASTQC&#10;N=( $(sed -n "${SGE_TASK_ID}p" $1) )&#10;R1=${N[0]}&#10;R2=${N[1]}&#10;# echo "fastqc $R1 $R2"&#10;fastqc $R1 $R2</pre>

@@ Line 11: / Line 11: @@
 # 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 $i; done</pre>
 # We need to generate a file listing of these files for later processing. The listing should reflecte the paired nature of the fastq files, and if they are named properly this should not be a problem and can be created with<pre>&#10;ls *.fastq.gz > fq.lst</pre>
-# then we can run a quality detection program, with themost widely used one being FASTQC. The following script will do each fastqc pair in parallel.<pre>&#10;#!/bin/bash&#10;#$ -cwd&#10;#$ -j y&#10;#$ -S /bin/bash&#10;#$ -V&#10;#$ -q marvin.q&#10;# some quick "argument accounting"&#10;EXPECTED_ARGS=1&#10;if [ $# -ne $EXPECTED_ARGS ]; then &#10;echo "error, this script should be fed with one argument: a filelist of fastq(.gz) files"&#10;exit&#10;fi&#10;module load FASTQC&#10;N=( $(sed -n "${SGE_TASK_ID}p" $1) )&#10;R1=${N[0]}&#10;R2=${N[1]}&#10;# echo "fastqc $R1 $R2"&#10;fastqc $R1 $R2</pre>
+# then we can run a quality detection program, with the most widely used one being Babraham Institute's FASTQC. The following script will do each fastqc pair in parallel.<pre>&#10;#!/bin/bash&#10;#$ -cwd&#10;#$ -j y&#10;#$ -S /bin/bash&#10;#$ -V&#10;#$ -q marvin.q&#10;# some quick "argument accounting"&#10;EXPECTED_ARGS=1&#10;if [ $# -ne $EXPECTED_ARGS ]; then &#10;echo "error, this script should be fed with one argument: a filelist of fastq(.gz) files"&#10;exit&#10;fi&#10;module load FASTQC&#10;N=( $(sed -n "${SGE_TASK_ID}p" $1) )&#10;R1=${N[0]}&#10;R2=${N[1]}&#10;# echo "fastqc $R1 $R2"&#10;fastqc $R1 $R2</pre>

@@ Line 10: / Line 10: @@
 # 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 $i; done</pre>
 # then we can run a quality detection program, with themost widely used one being FASTQC. The following script will do each fastqc pair in parallel.<pre>&#10;#!/bin/bash&#10;#$ -cwd&#10;#$ -j y&#10;#$ -S /bin/bash&#10;#$ -V&#10;#$ -q marvin.q&#10;# some quick "argument accounting"&#10;EXPECTED_ARGS=1&#10;if [ $# -ne $EXPECTED_ARGS ]; then &#10;echo "error, this script should be fed with one argument: a filelist of fastq(.gz) files"&#10;exit&#10;fi&#10;module load FASTQC&#10;N=( $(sed -n "${SGE_TASK_ID}p" $1) )&#10;R1=${N[0]}&#10;R2=${N[1]}&#10;# echo "fastqc $R1 $R2"&#10;fastqc $R1 $R2</pre>

@@ Line 10: / Line 10: @@
 # 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 $i; done</pre>
-# then we can run a quality detection program, with themost widely used one being FASTQC. The following script will do each fastqc pair in parallel.<pre>&#10;
+# then we can run a quality detection program, with themost widely used one being FASTQC. The following script will do each fastqc pair in parallel.<pre>&#10;#!/bin/bash&#10;#$ -cwd&#10;#$ -j y&#10;#$ -S /bin/bash&#10;#$ -V&#10;#$ -q marvin.q&#10;# some quick "argument accounting"&#10;EXPECTED_ARGS=1&#10;if [ $# -ne $EXPECTED_ARGS ]; then &#10;echo "error, this script should be fed with one argument: a filelist of fastq(.gz) files"&#10;exit&#10;fi&#10;module load FASTQC&#10;N=( $(sed -n "${SGE_TASK_ID}p" $1) )&#10;R1=${N[0]}&#10;R2=${N[1]}&#10;# echo "fastqc $R1 $R2"&#10;fastqc $R1 $R2</pre>

@@ Line 10: / Line 10: @@
 # 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 $i; done</pre>
-# then we can run a quality detection program, with themost widely used one being FASTQC. The following script will do each fastqc pair in parallel.
+# then we can run a quality detection program, with themost widely used one being FASTQC. The following script will do each fastqc pair in parallel.<pre>&#10;
   #!/bin/bash
   #$ -cwd
@@ Line 19: / Line 18: @@
   #$ -q marvin.q
-  # some quick "argument accounting"
+  # some quick "argument accounting"<pre>
   EXPECTED_ARGS=1 # change value to suit!
   if [ $# -ne $EXPECTED_ARGS ]; then
@@ Line 30: / Line 29: @@
   R2=${N[1]}
   # echo "fastqc $R1 $R2"
-  fastqc $R1 $R2
+  fastqc $R1 $R2</pre>

← Older revision		Revision as of 16:24, 18 July 2016
Line 11:		Line 11:
	# Create symlinks from your mounted directory to the new directory n scrathc you've just created. An example is:		# 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		for i in $(ls /storage/home/users/ramon/mnt/miseqda/2016-07-15_160715_M01714_0021_000000000-ANWN5/*.fastq.gz); do ln -s $i; done
		+
		+	# then we can run a quality detection program, witht emost widely used one being FASTQC. The following script will do each fastqc pair in parallel.
		+
		+
		+	#!/bin/bash
		+	#$ -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

@@ Line 3: / Line 3: @@
 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 unloaded onto HDRIVE.
+They are uploaded onto HDRIVE.
 = Procedure =