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Old 04-18-2017, 10:08 AM   #215
Brian Bushnell
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Location: Walnut Creek, CA

Join Date: Jan 2014
Posts: 2,707

The difference is primarily because you are quality-trimming to Q27, which is too high for almost any purpose. I'd suggest a command more like this:

Code: -Xmx8g in=D3_464_S2_L001_R1_001.fastq.gz out=D3_464_S2_L001_R1_001_trimmed.fastq.gz ref=resources/adapters.fa threads=8 k=19 mink=5 hdist=1 hdist2=0 ktrim=r qtrim=r minlength=36 trimq=14
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