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Old 01-15-2014, 11:13 AM   #3
Location: Georgia

Join Date: Apr 2013
Posts: 19

I like the idea of trimmomatic, but I can't seem to make it trim the adapters--they still show up after the following:

java -classpath /opt/Trimmomatic-0.32/trimmomatic-0.32.jar org.usadellab.trimmomatic.TrimmomaticPE -threads 8 -trimlog TT.log Pool1_S1_L001_R1_001.fastq Pool1_S1_L001_R2_001.fastq p1r1_TT.fastq p1r1_To.fastq p1r2_TT.fastq p1r2_To.fastq LEADING:3 TRAILING:3 ILLUMINACLIP:adapter_13.fa:2:30:10 SLIDINGWINDOW:4:15 MINLEN:16
I may have the parameters set funny, but I don't know the best way to set it. My adapter sequence is the 13bp common Illumina sequence--is 13bp not scoring high enough to get trimmed?
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