trimmomatic syntax help

[petrie]

Thank you!!!!!

[JackieBadger]

get rid of `which trimmomatic.jar`.... this is a command you use to locate files when you do not know the path.... seeing as this function returns the path, that is what you use

[petrie]

Hi! I am trying to use trimmomatic in palindrome mode to remove adaptor sequence from readthrough past the end of my fragment.
(My fragments are ~200 nt, and I sequenced with a 2X251 MiSeq run).
I am having trouble getting the syntax right. Below is command I'm using but I keep just getting a usage message, so I must be typing something in wrong.

I'm a bench scientist in the process of learning coding by doing, so I'd really appreciate it if anyone could help me spot the noob error. Thanks!

java -jar `which trimmomatic.jar` /opt/applications/trimmomatic/0.30/trimmomatic.jar
PE -phred33 -trimlog 092713log1.log
2013-5_S5_L001_R1_001.fastq 2013-5_S5_L001_R2_001.fastq 092713pairedR1.fastq 092713unpairedR1.fastq
092713pairedR2.fastq 092713unpariedR2.fastq ILLUMINACLIP:Nexterai7Multiplex2_PE_barcode5.fasta:4:30:7:1:true

Here's the error I get back. I assume it's the program's way of informing me that I am entering the parameters incorrectly.

Usage:
PE [-threads <threads>] [-phred33|-phred64] [-trimlog <trimLogFile>] <inputFile1> <inputFile2> <outputFile1P> <outputFile1U> <outputFile2P> <outputFile2U> <trimmer1>...
or:
SE [-threads <threads>] [-phred33|-phred64] [-trimlog <trimLogFile>] <inputFile> <outputFile> <trimmer1>...