Hi, all I have Double End fastq file and it needs trimming. So, I use trimmomatic software for this purpose.based on trimmomatic tutorial I write below code for my .fq.gz file:
!/bin/bash
PBS -N 04.trimmomatic
PBS -l nodes=1:ppn=10
PBS -j oe
PBS -q middle
cw=/histor/kang/guowei/lhr/dataanalysis/04.trimmomatic cd $cw/
data=/histor/kang/guowei/lhr/trinity/ALL_DATA i=GT1-N2 adapter=/histor/kang/guowei/lhr/software/trimmomatic/Trimmomatic-0.39/adapters/TruSeq4-PE.fa trimmomatic=/histor/kang/guowei/lhr/software/trimmomatic/Trimmomatic-0.39/trimmomatic-0.39.jar
java -jar $trimmomatic PE -threads 10 -phred33 $data/$i/_fq.gz $data/$i/_fq.gz $i.paired_GT1-N2_FRAS210028606-2r_1_fq.gz $i.unpaired_GT1-N2_FRAS210028606-2r_1_fq.gz $i.paired_GT1-N2_FRAS210028606-2r_2_fq.gz $i.unpaired_GT1-N2_FRAS210028606-2r_2_fq.gz ILLUMINACLIP:$adapter:2:30:10 LEADING:5 TRAILING:5 SLIDINGWINDOW:4:5 MINLEN:25 -trimlog trim2.log
but after run it in my Terminal, I see bellow error; Exception in thread "main" java.lang.RuntimeException: Unknown trimmer: GT1-N1.paired_GT1-N1_FRAS210028605-2r_2.fq.gz
