Trimmomatic - Revision history

Rf at 17:17, 5 July 2016

2016-07-05T17:17:57Z

Rf at 17:06, 5 July 2016

2016-07-05T17:06:57Z

Rf at 17:05, 5 July 2016

2016-07-05T17:05:58Z

Rf at 14:54, 5 July 2016

2016-07-05T14:54:47Z

Rf: Created page with "=Introduction= = Example use-cases= java -jar $PATHTRIMMOJAR/trimmomatic-0.32.jar PE -threads 6 -phred33 $DATASETPATH/Pair1.fastq.gz $DATASETPATH/Pair1.fastq.gz forward_pai..."

2016-06-29T16:12:58Z

Created page with "=Introduction= = Example use-cases= java -jar $PATHTRIMMOJAR/trimmomatic-0.32.jar PE -threads 6 -phred33 $DATASETPATH/Pair1.fastq.gz $DATASETPATH/Pair1.fastq.gz forward_pai..."

New page

=Introduction=

= Example use-cases=

java -jar $PATHTRIMMOJAR/trimmomatic-0.32.jar PE -threads 6 -phred33 $DATASETPATH/Pair1.fastq.gz $DATASETPATH/Pair1.fastq.gz forward_paired.fq forward_unpaired.fq reverse_paired.fq reverse_unpaired.fq ILLUMINACLIP:TruSeq3-PE.fa:2:30:10 LEADING:5 TRAILING:5 SLIDINGWINDOW:4:15 MINLEN:50

@@ Line 7: / Line 7: @@
 Trimmomatic is quite unique in the way it is called.
-It is a java program, so this requires the jar file naturally, and then:
+It is a java program, so this requires the jar file (naturally) and then:
 # whether single- or pair-end reads (SE|PE)
 # number of threads with hyphen, i.e. -threads N
-# whether quality scoring is phred33 or phred64 (although it will try to detect)
+# whether quality scoring is phred33 or phred64 (although it will try to auto-detect)
+# next come the two input pair-ended file with no hyphens, i.e just the plain filenames.
 == Adapter file specification ==

@@ Line 16: / Line 16: @@
 == Adapter file specification ==
-You can use an environmental variable for the adapter fasta file, because they have been set by the module and will point to the right place.
+You can use an environmental variable for the adapter fasta file, because they have been set by the module and will point to the right place. Here is a list, the most commonly used one is $TS3PE.
 * $TS3SE is TruSeq3-SE.fa
@@ Line 24: / Line 24: @@
 * $TS3PE is TruSeq3-PE.fa
 * $TS3PE2 is TruSeq3-PE-2.fa
 == Example use-cases==
   java -jar $PATHTRIMMOJAR/trimmomatic-0.32.jar PE -threads 6 -phred33 $DATASETPATH/Pair1.fastq.gz $DATASETPATH/Pair1.fastq.gz forward_paired.fq forward_unpaired.fq reverse_paired.fq reverse_unpaired.fq ILLUMINACLIP:$TS3PE:2:30:10 LEADING:5 TRAILING:5 SLIDINGWINDOW:4:15 MINLEN:50

@@ Line 12: / Line 12: @@
 # number of threads with hyphen, i.e. -threads N
 # whether quality scoring is phred33 or phred64 (although it will try to detect)
 * $TS3SE is TruSeq3-SE.fa
@@ Line 23: / Line 28: @@
 == Example use-cases==
-  java -jar $PATHTRIMMOJAR/trimmomatic-0.32.jar PE -threads 6 -phred33 $DATASETPATH/Pair1.fastq.gz $DATASETPATH/Pair1.fastq.gz forward_paired.fq forward_unpaired.fq reverse_paired.fq reverse_unpaired.fq ILLUMINACLIP:TruSeq3-PE.fa:2:30:10 LEADING:5 TRAILING:5 SLIDINGWINDOW:4:15 MINLEN:50
+  java -jar $PATHTRIMMOJAR/trimmomatic-0.32.jar PE -threads 6 -phred33 $DATASETPATH/Pair1.fastq.gz $DATASETPATH/Pair1.fastq.gz forward_paired.fq forward_unpaired.fq reverse_paired.fq reverse_unpaired.fq ILLUMINACLIP:$TS3PE:2:30:10 LEADING:5 TRAILING:5 SLIDINGWINDOW:4:15 MINLEN:50

@@ Line 1: / Line 1: @@
 =Introduction=
-= Example use-cases=
+Another tool for quality trimming ... this is probably the best known.
   java -jar $PATHTRIMMOJAR/trimmomatic-0.32.jar PE -threads 6 -phred33 $DATASETPATH/Pair1.fastq.gz $DATASETPATH/Pair1.fastq.gz forward_paired.fq forward_unpaired.fq reverse_paired.fq reverse_unpaired.fq ILLUMINACLIP:TruSeq3-PE.fa:2:30:10 LEADING:5 TRAILING:5 SLIDINGWINDOW:4:15 MINLEN:50