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eanbit-rt / mini-projects-19

Mini-projects for the residential training
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using trimmomatic on HPCh #10

Closed henrick-aduda closed 5 years ago

henrick-aduda commented 5 years ago

Trying to use trimmomatic on the HPC but its a bit troublesome. Anyone with an idea on how to use trimmomatic on the hpc. This is what i tried out : java -jar $TRIMMOJAR PE -phred33 \ /home/user11/sampe1_read1.fastq.gz /home/user11/sample1_read2.fastq.gz \ output_forward_paired.fq.gz output_forward_unpaired.fq.gz \ output_reverse_paired.fq.gz output_reverse_unpaired.fq.gz \ ILLUMINACLIP:../export/apps/trimmomatic/0.33/trimmomatic/adapters/TruSeq3-PE.fa:2:30:10 LEADING:3 TRAILING:3 SLIDINGWINDOW:4:15 MINLEN:36 @kipkurui

kipkurui commented 5 years ago

Hey @henrick-aduda, what is the error message you are encountering?

henrick-aduda commented 5 years ago

Hey @kipkurui i finally figured it out. we had a session on monday with Etienne and that shed some light on what was going on. Turns out i did not need to put in the directory to my input folders when running the trimmomatic command. Also i was running it earlier on the HPC without module loading trimmomatic