Difference between revisions of "Trimmomatic"
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# number of threads with hyphen, i.e. -threads N | # 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 detect) | ||
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| + | == 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. | ||
* $TS3SE is TruSeq3-SE.fa | * $TS3SE is TruSeq3-SE.fa | ||
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== Example use-cases== | == 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: | + | 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 |
Revision as of 17:05, 5 July 2016
Introduction
Another tool for quality trimming ... this is probably the best known.
Usage
Trimmomatic is quite unique in the way it is called.
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)
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.
- $TS3SE is TruSeq3-SE.fa
- $TS2SE is TruSeq2-SE.fa
- $TS2PE is TruSeq2-PE.fa
- $NXPE is NexteraPE-PE.fa
- $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
