Difference between revisions of "HPC:Trimmomatic"
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(Created page with "=== Trimmomatic === Trimmomatic is a tool for trimming Illumina FASTQ data and removing adapters. It performs a variety of useful trimming tasks for illumina paired-end and si...") |
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<pre> | <pre> | ||
[asrini@node107 ~]$ module load Trimmomatic-0.32 | [asrini@node107 ~]$ module load Trimmomatic-0.32 | ||
| + | </pre> | ||
| − | [asrini@node107 ~]$ | + | The above module load command sets the $TRIM_JAR environment variable. |
| + | |||
| + | <pre> | ||
| + | [asrini@node107 ~]$ echo $TRIM_JAR | ||
| + | /opt/software/Trimmomatic/0.32/trimmomatic-0.32.jar | ||
| + | </pre> | ||
| + | |||
| + | This environment variable can be used by passing it directly to the java command: | ||
| + | <pre> | ||
| + | [asrini@node107 ~]$ java -jar $TRIM_JAR | ||
Usage: | Usage: | ||
PE [-threads <threads>] [-phred33|-phred64] [-trimlog <trimLogFile>] [-basein <inputBase> | <inputFile1> <inputFile2>] [-baseout <outputBase> | <outputFile1P> <outputFile1U> <outputFile2P> <outputFile2U>] <trimmer1>... | PE [-threads <threads>] [-phred33|-phred64] [-trimlog <trimLogFile>] [-basein <inputBase> | <inputFile1> <inputFile2>] [-baseout <outputBase> | <outputFile1P> <outputFile1U> <outputFile2P> <outputFile2U>] <trimmer1>... | ||
or: | or: | ||
SE [-threads <threads>] [-phred33|-phred64] [-trimlog <trimLogFile>] <inputFile> <outputFile> <trimmer1>... | SE [-threads <threads>] [-phred33|-phred64] [-trimlog <trimLogFile>] <inputFile> <outputFile> <trimmer1>... | ||
| − | |||
</pre> | </pre> | ||
=== Other Pages === | === Other Pages === | ||
| + | ---- | ||
| + | <div class="mw-collapsible mw-collapsed"> | ||
| + | *[[HPC:FAQ|HPC FAQ ]] | ||
| + | *[[HPC:Login|Connecting to the PMACS cluster]] | ||
| + | *[[HPC:User_Guide|User Guide]] | ||
*[[HPC:Software|Available Software]] | *[[HPC:Software|Available Software]] | ||
| − | *[[HPC: | + | *[[HPC:Archive System|PMACS Archive System]] |
| − | + | </div> | |
| − | |||
Latest revision as of 15:49, 13 August 2019
Trimmomatic
Trimmomatic is a tool for trimming Illumina FASTQ data and removing adapters. It performs a variety of useful trimming tasks for illumina paired-end and single ended data. The selection of trimming steps and their associated parameters are supplied on the command line. Trimmomatic version 0.32 is installed across all HPC nodes and is made available via a module file.
[asrini@node107 ~]$ module load Trimmomatic-0.32
The above module load command sets the $TRIM_JAR environment variable.
[asrini@node107 ~]$ echo $TRIM_JAR /opt/software/Trimmomatic/0.32/trimmomatic-0.32.jar
This environment variable can be used by passing it directly to the java command:
[asrini@node107 ~]$ java -jar $TRIM_JAR
Usage:
PE [-threads <threads>] [-phred33|-phred64] [-trimlog <trimLogFile>] [-basein <inputBase> | <inputFile1> <inputFile2>] [-baseout <outputBase> | <outputFile1P> <outputFile1U> <outputFile2P> <outputFile2U>] <trimmer1>...
or:
SE [-threads <threads>] [-phred33|-phred64] [-trimlog <trimLogFile>] <inputFile> <outputFile> <trimmer1>...
